Starting phenix.real_space_refine on Tue Feb 13 15:55:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddf_7869/02_2024/6ddf_7869_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddf_7869/02_2024/6ddf_7869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddf_7869/02_2024/6ddf_7869.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddf_7869/02_2024/6ddf_7869.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddf_7869/02_2024/6ddf_7869_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddf_7869/02_2024/6ddf_7869_neut_updated.pdb" } resolution = 3.5 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= 0.021 sd= 0.567 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 52 5.16 5 C 4342 2.51 5 N 1165 2.21 5 O 1249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 242": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "R TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 179": "NH1" <-> "NH2" Residue "R ARG 263": "NH1" <-> "NH2" Residue "R ARG 273": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6808 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1694 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2547 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 396 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "R" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2134 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 270} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 37 Unusual residues: {'ETA': 1} Classifications: {'peptide': 4, 'undetermined': 1} Modifications used: {'PEPT-D': 1} Link IDs: {'LINK_CpN': 1, 'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 4.16, per 1000 atoms: 0.61 Number of scatterers: 6808 At special positions: 0 Unit cell: (76.96, 118.56, 112.32, 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 52 16.00 O 1249 8.00 N 1165 7.00 C 4342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 140 " - pdb=" SG CYS R 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.4 seconds 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL D 2 " Number of C-beta restraints generated: 1686 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 9 sheets defined 37.1% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 9 through 32 removed outlier: 3.711A pdb=" N ASP A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 277 removed outlier: 5.163A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 310 removed outlier: 3.834A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.720A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 24 removed outlier: 3.601A pdb=" N ASP B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 23 Processing helix chain 'C' and resid 35 through 42 removed outlier: 3.672A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 96 removed outlier: 4.500A pdb=" N VAL R 78 " --> pdb=" O LEU R 74 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N CYS R 79 " --> pdb=" O TYR R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 129 removed outlier: 3.598A pdb=" N TYR R 106 " --> pdb=" O ALA R 102 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA R 117 " --> pdb=" O ALA R 113 " (cutoff:3.500A) Proline residue: R 122 - end of helix removed outlier: 3.627A pdb=" N SER R 125 " --> pdb=" O LEU R 121 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL R 126 " --> pdb=" O PRO R 122 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN R 127 " --> pdb=" O PHE R 123 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR R 128 " --> pdb=" O GLN R 124 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU R 129 " --> pdb=" O SER R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 170 removed outlier: 4.238A pdb=" N LYS R 141 " --> pdb=" O ASN R 137 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ILE R 142 " --> pdb=" O ILE R 138 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE R 152 " --> pdb=" O TYR R 148 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU R 158 " --> pdb=" O SER R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 178 removed outlier: 3.921A pdb=" N LEU R 176 " --> pdb=" O PRO R 172 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP R 177 " --> pdb=" O VAL R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 205 removed outlier: 3.612A pdb=" N ILE R 198 " --> pdb=" O LEU R 194 " (cutoff:3.500A) Proline residue: R 201 - end of helix removed outlier: 4.191A pdb=" N MET R 205 " --> pdb=" O PRO R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 230 through 240 removed outlier: 3.936A pdb=" N ILE R 234 " --> pdb=" O ASN R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 242 through 248 Processing helix chain 'R' and resid 250 through 261 removed outlier: 4.254A pdb=" N MET R 255 " --> pdb=" O CYS R 251 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER R 261 " --> pdb=" O LEU R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 293 Processing helix chain 'R' and resid 295 through 305 removed outlier: 3.826A pdb=" N VAL R 300 " --> pdb=" O ILE R 296 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA R 304 " --> pdb=" O VAL R 300 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU R 305 " --> pdb=" O ILE R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 314 through 336 removed outlier: 4.468A pdb=" N ASN R 328 " --> pdb=" O LEU R 324 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER R 329 " --> pdb=" O GLY R 325 " (cutoff:3.500A) Proline residue: R 333 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 220 through 224 removed outlier: 3.876A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 111 through 113 removed outlier: 3.613A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 123 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.721A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 220 through 223 removed outlier: 3.987A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 250 through 254 Processing sheet with id= F, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.876A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.854A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 78 through 82 removed outlier: 3.615A pdb=" N LEU B 79 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 315 through 320 removed outlier: 6.910A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1369 1.33 - 1.45: 1722 1.45 - 1.58: 3779 1.58 - 1.70: 0 1.70 - 1.82: 75 Bond restraints: 6945 Sorted by residual: bond pdb=" C MEA D 4 " pdb=" N ETA D 5 " ideal model delta sigma weight residual 1.329 1.429 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C LEU B 79 " pdb=" O LEU B 79 " ideal model delta sigma weight residual 1.236 1.203 0.033 1.24e-02 6.50e+03 7.30e+00 bond pdb=" CA LEU B 79 " pdb=" CB LEU B 79 " ideal model delta sigma weight residual 1.528 1.500 0.028 1.35e-02 5.49e+03 4.34e+00 bond pdb=" CB PRO R 244 " pdb=" CG PRO R 244 " ideal model delta sigma weight residual 1.492 1.392 0.100 5.00e-02 4.00e+02 4.01e+00 bond pdb=" CA LEU B 79 " pdb=" C LEU B 79 " ideal model delta sigma weight residual 1.524 1.504 0.021 1.22e-02 6.72e+03 2.88e+00 ... (remaining 6940 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.84: 112 105.84 - 112.91: 3683 112.91 - 119.98: 2526 119.98 - 127.05: 3025 127.05 - 134.12: 84 Bond angle restraints: 9430 Sorted by residual: angle pdb=" N LEU R 121 " pdb=" CA LEU R 121 " pdb=" C LEU R 121 " ideal model delta sigma weight residual 109.81 120.78 -10.97 2.21e+00 2.05e-01 2.46e+01 angle pdb=" C SER R 268 " pdb=" N LYS R 269 " pdb=" CA LYS R 269 " ideal model delta sigma weight residual 121.54 129.84 -8.30 1.91e+00 2.74e-01 1.89e+01 angle pdb=" N MEA D 4 " pdb=" CA MEA D 4 " pdb=" CB MEA D 4 " ideal model delta sigma weight residual 110.50 117.47 -6.97 1.70e+00 3.46e-01 1.68e+01 angle pdb=" C ASP B 27 " pdb=" N ALA B 28 " pdb=" CA ALA B 28 " ideal model delta sigma weight residual 121.19 127.29 -6.10 1.59e+00 3.96e-01 1.47e+01 angle pdb=" N LEU B 79 " pdb=" CA LEU B 79 " pdb=" C LEU B 79 " ideal model delta sigma weight residual 108.96 103.24 5.72 1.59e+00 3.96e-01 1.29e+01 ... (remaining 9425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.19: 3676 12.19 - 24.39: 324 24.39 - 36.58: 73 36.58 - 48.78: 27 48.78 - 60.97: 1 Dihedral angle restraints: 4101 sinusoidal: 1501 harmonic: 2600 Sorted by residual: dihedral pdb=" CA ILE A 49 " pdb=" C ILE A 49 " pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta harmonic sigma weight residual 180.00 150.50 29.50 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA SER R 214 " pdb=" C SER R 214 " pdb=" N ILE R 215 " pdb=" CA ILE R 215 " ideal model delta harmonic sigma weight residual 180.00 151.00 29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 151.90 28.10 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 4098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 796 0.057 - 0.113: 251 0.113 - 0.170: 41 0.170 - 0.227: 7 0.227 - 0.284: 3 Chirality restraints: 1098 Sorted by residual: chirality pdb=" CB ILE R 308 " pdb=" CA ILE R 308 " pdb=" CG1 ILE R 308 " pdb=" CG2 ILE R 308 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA LEU R 121 " pdb=" N LEU R 121 " pdb=" C LEU R 121 " pdb=" CB LEU R 121 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB ILE B 37 " pdb=" CA ILE B 37 " pdb=" CG1 ILE B 37 " pdb=" CG2 ILE B 37 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1095 not shown) Planarity restraints: 1190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 63 " 0.014 2.00e-02 2.50e+03 1.66e-02 6.88e+00 pdb=" CG TRP B 63 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP B 63 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP B 63 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 63 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 63 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 63 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 63 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 63 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP B 63 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO C 49 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 180 " -0.039 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO R 181 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO R 181 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO R 181 " -0.032 5.00e-02 4.00e+02 ... (remaining 1187 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1192 2.76 - 3.30: 6378 3.30 - 3.83: 11330 3.83 - 4.37: 12807 4.37 - 4.90: 22150 Nonbonded interactions: 53857 Sorted by model distance: nonbonded pdb=" NZ LYS A 210 " pdb=" OD2 ASP B 246 " model vdw 2.228 2.520 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.259 2.440 nonbonded pdb=" OD1 ASP R 147 " pdb=" OH TYR R 326 " model vdw 2.283 2.440 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.310 2.440 nonbonded pdb=" N THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.313 2.520 ... (remaining 53852 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.680 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: 3.330 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 21.720 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 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 0.100 6945 Z= 0.406 Angle : 1.014 10.968 9430 Z= 0.540 Chirality : 0.057 0.284 1098 Planarity : 0.007 0.065 1190 Dihedral : 10.484 60.972 2412 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.34 % Favored : 91.54 % Rotamer: Outliers : 0.72 % Allowed : 5.15 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -4.62 (0.23), residues: 875 helix: -2.94 (0.19), residues: 347 sheet: -3.53 (0.36), residues: 159 loop : -2.74 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP B 63 HIS 0.011 0.002 HIS B 183 PHE 0.031 0.003 PHE B 241 TYR 0.031 0.003 TYR R 299 ARG 0.004 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 246 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7114 (t70) cc_final: 0.6641 (t0) REVERT: B 65 THR cc_start: 0.7469 (p) cc_final: 0.7212 (p) REVERT: B 78 LYS cc_start: 0.8230 (mmpt) cc_final: 0.7742 (mmtt) REVERT: B 123 ILE cc_start: 0.8588 (pp) cc_final: 0.8376 (pt) REVERT: R 162 SER cc_start: 0.8137 (t) cc_final: 0.7889 (t) REVERT: R 198 ILE cc_start: 0.3926 (tp) cc_final: 0.3041 (mt) REVERT: R 216 ASP cc_start: 0.7316 (t0) cc_final: 0.6711 (t0) REVERT: R 336 TYR cc_start: 0.7601 (m-10) cc_final: 0.7219 (m-80) outliers start: 5 outliers final: 1 residues processed: 250 average time/residue: 0.2193 time to fit residues: 69.1426 Evaluate side-chains 161 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 79 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 244 HIS A 269 ASN A 294 ASN B 13 GLN B 88 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 HIS R 314 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6945 Z= 0.176 Angle : 0.638 9.276 9430 Z= 0.324 Chirality : 0.041 0.130 1098 Planarity : 0.004 0.040 1190 Dihedral : 5.931 65.565 960 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.86 % Allowed : 15.88 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.32 (0.26), residues: 875 helix: -1.22 (0.25), residues: 345 sheet: -3.29 (0.35), residues: 170 loop : -2.47 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.012 0.001 PHE R 87 TYR 0.016 0.001 TYR R 149 ARG 0.006 0.001 ARG R 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 188 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 200 VAL cc_start: 0.8951 (OUTLIER) cc_final: 0.8525 (m) REVERT: B 234 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7628 (m-10) REVERT: C 32 LYS cc_start: 0.7724 (tppt) cc_final: 0.7326 (mttt) outliers start: 27 outliers final: 15 residues processed: 208 average time/residue: 0.2139 time to fit residues: 56.9597 Evaluate side-chains 173 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 290 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 0.0470 chunk 65 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 269 ASN B 13 GLN B 32 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 119 ASN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 314 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6945 Z= 0.163 Angle : 0.619 9.570 9430 Z= 0.311 Chirality : 0.041 0.129 1098 Planarity : 0.004 0.035 1190 Dihedral : 5.515 66.606 960 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.15 % Allowed : 19.74 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.67 (0.28), residues: 875 helix: -0.50 (0.27), residues: 343 sheet: -3.07 (0.36), residues: 161 loop : -2.29 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.021 0.001 PHE B 222 TYR 0.017 0.001 TYR R 149 ARG 0.006 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 183 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 200 VAL cc_start: 0.8944 (OUTLIER) cc_final: 0.8434 (m) REVERT: B 234 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7516 (m-10) REVERT: R 293 TRP cc_start: 0.7828 (OUTLIER) cc_final: 0.6829 (m-10) REVERT: R 306 ILE cc_start: 0.3027 (OUTLIER) cc_final: 0.2745 (tt) outliers start: 36 outliers final: 20 residues processed: 204 average time/residue: 0.1961 time to fit residues: 51.8299 Evaluate side-chains 183 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 0.0470 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS B 13 GLN B 32 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6945 Z= 0.197 Angle : 0.609 9.925 9430 Z= 0.310 Chirality : 0.041 0.128 1098 Planarity : 0.004 0.031 1190 Dihedral : 5.296 62.970 960 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 5.58 % Allowed : 19.74 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.28 (0.28), residues: 875 helix: -0.17 (0.27), residues: 346 sheet: -2.95 (0.38), residues: 143 loop : -2.14 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.024 0.002 PHE B 222 TYR 0.017 0.001 TYR R 149 ARG 0.005 0.001 ARG R 182 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 166 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6751 (tt) REVERT: B 234 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7711 (m-10) REVERT: R 83 LEU cc_start: 0.6661 (tm) cc_final: 0.6175 (tm) REVERT: R 293 TRP cc_start: 0.7815 (OUTLIER) cc_final: 0.6835 (m-10) outliers start: 39 outliers final: 22 residues processed: 189 average time/residue: 0.1956 time to fit residues: 48.0313 Evaluate side-chains 185 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 230 ASN C 18 GLN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 6945 Z= 0.414 Angle : 0.742 11.232 9430 Z= 0.380 Chirality : 0.045 0.159 1098 Planarity : 0.004 0.034 1190 Dihedral : 5.793 51.700 960 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 6.29 % Allowed : 21.46 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.46 (0.28), residues: 875 helix: -0.41 (0.27), residues: 345 sheet: -2.77 (0.37), residues: 161 loop : -2.18 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 169 HIS 0.007 0.001 HIS B 183 PHE 0.030 0.002 PHE R 87 TYR 0.016 0.002 TYR R 148 ARG 0.006 0.001 ARG R 182 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 160 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: B 78 LYS cc_start: 0.8314 (mmpt) cc_final: 0.7609 (mmtt) REVERT: B 117 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7388 (tt) REVERT: B 164 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7631 (p) REVERT: B 234 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7888 (m-10) REVERT: R 293 TRP cc_start: 0.7994 (OUTLIER) cc_final: 0.7027 (m-10) REVERT: R 306 ILE cc_start: 0.3674 (OUTLIER) cc_final: 0.3434 (tt) outliers start: 44 outliers final: 25 residues processed: 191 average time/residue: 0.1959 time to fit residues: 48.6426 Evaluate side-chains 169 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 162 SER Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.1980 chunk 16 optimal weight: 0.2980 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 44 optimal weight: 0.0980 chunk 81 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 13 GLN B 91 HIS B 230 ASN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6945 Z= 0.168 Angle : 0.632 8.280 9430 Z= 0.319 Chirality : 0.042 0.198 1098 Planarity : 0.004 0.031 1190 Dihedral : 5.386 67.169 960 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.86 % Allowed : 25.46 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.00 (0.29), residues: 875 helix: 0.04 (0.28), residues: 343 sheet: -2.69 (0.38), residues: 148 loop : -1.97 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 339 HIS 0.004 0.001 HIS B 142 PHE 0.028 0.001 PHE B 222 TYR 0.018 0.001 TYR R 149 ARG 0.007 0.001 ARG R 263 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 161 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8424 (tp) REVERT: B 75 GLN cc_start: 0.7302 (mm110) cc_final: 0.6885 (mm-40) REVERT: B 78 LYS cc_start: 0.8148 (mmpt) cc_final: 0.7476 (mmtm) REVERT: B 164 THR cc_start: 0.7707 (OUTLIER) cc_final: 0.7254 (p) REVERT: B 234 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7724 (m-10) REVERT: R 293 TRP cc_start: 0.7971 (OUTLIER) cc_final: 0.6801 (m-10) outliers start: 34 outliers final: 14 residues processed: 181 average time/residue: 0.1978 time to fit residues: 46.7580 Evaluate side-chains 168 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 50 optimal weight: 0.0770 chunk 25 optimal weight: 5.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 230 ASN B 266 HIS ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6945 Z= 0.200 Angle : 0.636 9.824 9430 Z= 0.318 Chirality : 0.042 0.162 1098 Planarity : 0.004 0.032 1190 Dihedral : 5.287 65.001 960 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.15 % Allowed : 26.90 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.74 (0.29), residues: 875 helix: 0.24 (0.28), residues: 343 sheet: -2.30 (0.39), residues: 151 loop : -1.92 (0.34), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 339 HIS 0.006 0.001 HIS B 142 PHE 0.029 0.001 PHE B 222 TYR 0.015 0.001 TYR R 149 ARG 0.006 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 155 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8396 (tp) REVERT: B 78 LYS cc_start: 0.8056 (mmpt) cc_final: 0.7424 (mmtm) REVERT: B 164 THR cc_start: 0.7797 (OUTLIER) cc_final: 0.7304 (p) REVERT: B 200 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8439 (m) REVERT: B 234 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7683 (m-10) REVERT: C 32 LYS cc_start: 0.7762 (mtmt) cc_final: 0.7452 (mttt) REVERT: R 293 TRP cc_start: 0.7965 (OUTLIER) cc_final: 0.6923 (m-10) outliers start: 29 outliers final: 17 residues processed: 174 average time/residue: 0.2023 time to fit residues: 45.4210 Evaluate side-chains 172 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 0.0270 chunk 53 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 256 ASN A 269 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6945 Z= 0.231 Angle : 0.652 9.527 9430 Z= 0.326 Chirality : 0.043 0.159 1098 Planarity : 0.004 0.033 1190 Dihedral : 5.276 62.968 960 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 5.15 % Allowed : 26.04 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.68 (0.29), residues: 875 helix: 0.20 (0.28), residues: 350 sheet: -2.13 (0.40), residues: 156 loop : -1.87 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 339 HIS 0.006 0.001 HIS B 142 PHE 0.026 0.001 PHE B 222 TYR 0.015 0.001 TYR R 149 ARG 0.007 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 152 time to evaluate : 0.788 Fit side-chains REVERT: A 33 GLU cc_start: 0.7572 (tt0) cc_final: 0.7236 (tt0) REVERT: B 78 LYS cc_start: 0.8071 (mmpt) cc_final: 0.7438 (mmtm) REVERT: B 164 THR cc_start: 0.7799 (OUTLIER) cc_final: 0.7272 (p) REVERT: B 200 VAL cc_start: 0.9080 (OUTLIER) cc_final: 0.8393 (m) REVERT: B 234 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7643 (m-10) REVERT: C 32 LYS cc_start: 0.7833 (mtmt) cc_final: 0.7503 (mttt) REVERT: R 293 TRP cc_start: 0.7948 (OUTLIER) cc_final: 0.7053 (m-10) outliers start: 36 outliers final: 23 residues processed: 174 average time/residue: 0.2008 time to fit residues: 45.2974 Evaluate side-chains 169 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 142 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 256 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 230 ASN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6945 Z= 0.231 Angle : 0.667 9.765 9430 Z= 0.333 Chirality : 0.043 0.163 1098 Planarity : 0.004 0.033 1190 Dihedral : 5.303 64.059 960 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.01 % Allowed : 27.04 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.69 (0.29), residues: 875 helix: 0.22 (0.28), residues: 350 sheet: -2.22 (0.40), residues: 156 loop : -1.87 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 339 HIS 0.006 0.001 HIS B 142 PHE 0.028 0.002 PHE B 222 TYR 0.015 0.001 TYR R 149 ARG 0.007 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 0.817 Fit side-chains REVERT: A 33 GLU cc_start: 0.7535 (tt0) cc_final: 0.7300 (tt0) REVERT: B 78 LYS cc_start: 0.8042 (mmpt) cc_final: 0.7437 (mmtm) REVERT: B 164 THR cc_start: 0.7748 (OUTLIER) cc_final: 0.7446 (p) REVERT: B 200 VAL cc_start: 0.9075 (OUTLIER) cc_final: 0.8395 (m) REVERT: B 234 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7644 (m-10) REVERT: C 32 LYS cc_start: 0.7804 (mtmt) cc_final: 0.7488 (mttt) REVERT: R 293 TRP cc_start: 0.7949 (OUTLIER) cc_final: 0.7047 (m-10) outliers start: 28 outliers final: 20 residues processed: 165 average time/residue: 0.1939 time to fit residues: 42.0508 Evaluate side-chains 169 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 145 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 0.0770 chunk 79 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 0.2980 chunk 54 optimal weight: 0.3980 chunk 73 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 256 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 266 HIS ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6945 Z= 0.169 Angle : 0.645 10.443 9430 Z= 0.318 Chirality : 0.042 0.174 1098 Planarity : 0.004 0.032 1190 Dihedral : 5.224 67.849 960 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.01 % Allowed : 27.04 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.58 (0.29), residues: 875 helix: 0.37 (0.28), residues: 350 sheet: -2.33 (0.40), residues: 151 loop : -1.81 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 339 HIS 0.005 0.001 HIS B 142 PHE 0.027 0.001 PHE B 222 TYR 0.016 0.001 TYR R 149 ARG 0.007 0.001 ARG B 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 0.851 Fit side-chains REVERT: A 33 GLU cc_start: 0.7438 (tt0) cc_final: 0.7214 (tt0) REVERT: B 78 LYS cc_start: 0.8015 (mmpt) cc_final: 0.7413 (mmtm) REVERT: B 164 THR cc_start: 0.7631 (OUTLIER) cc_final: 0.7349 (p) REVERT: B 200 VAL cc_start: 0.9043 (OUTLIER) cc_final: 0.8564 (m) REVERT: B 234 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7760 (m-10) REVERT: C 32 LYS cc_start: 0.7700 (mtmt) cc_final: 0.7446 (mttt) REVERT: R 293 TRP cc_start: 0.7915 (OUTLIER) cc_final: 0.6992 (m-10) outliers start: 28 outliers final: 17 residues processed: 165 average time/residue: 0.1999 time to fit residues: 43.4939 Evaluate side-chains 162 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 70 optimal weight: 0.0970 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 266 HIS ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.136073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.114994 restraints weight = 11809.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.119461 restraints weight = 6179.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.122519 restraints weight = 3816.314| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6945 Z= 0.184 Angle : 0.642 9.915 9430 Z= 0.319 Chirality : 0.042 0.171 1098 Planarity : 0.004 0.032 1190 Dihedral : 5.197 66.664 960 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.72 % Allowed : 27.47 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.49 (0.29), residues: 875 helix: 0.46 (0.28), residues: 350 sheet: -2.20 (0.42), residues: 139 loop : -1.86 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 82 HIS 0.005 0.001 HIS B 142 PHE 0.029 0.001 PHE B 222 TYR 0.016 0.001 TYR R 149 ARG 0.007 0.001 ARG B 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1833.70 seconds wall clock time: 33 minutes 56.15 seconds (2036.15 seconds total)