Starting phenix.real_space_refine on Wed Sep 25 17:09:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgx_31979/09_2024/7vgx_31979.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgx_31979/09_2024/7vgx_31979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgx_31979/09_2024/7vgx_31979.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgx_31979/09_2024/7vgx_31979.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgx_31979/09_2024/7vgx_31979.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgx_31979/09_2024/7vgx_31979.cif" } resolution = 3.2 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= 0.035 sd= 0.132 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2157 atoms to isotropic. 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 66 5.16 5 C 5763 2.51 5 N 1540 2.21 5 O 1675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9044 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2257 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 268} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 200 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain breaks: 1 Chain: "A" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1806 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "S" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1762 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 6.61, per 1000 atoms: 0.73 Number of scatterers: 9044 At special positions: 0 Unit cell: (93.42, 121.965, 140.13, 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 66 16.00 O 1675 8.00 N 1540 7.00 C 5763 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 113 " - pdb=" SG CYS R 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.05 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 37.1% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'R' and resid 36 through 68 removed outlier: 3.750A pdb=" N ILE R 40 " --> pdb=" O PRO R 36 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE R 41 " --> pdb=" O LEU R 37 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN R 68 " --> pdb=" O ILE R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 103 removed outlier: 3.570A pdb=" N ILE R 77 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU R 94 " --> pdb=" O ALA R 90 " (cutoff:3.500A) Proline residue: R 95 - end of helix removed outlier: 3.797A pdb=" N PHE R 98 " --> pdb=" O LEU R 94 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL R 99 " --> pdb=" O PRO R 95 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU R 102 " --> pdb=" O PHE R 98 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET R 103 " --> pdb=" O VAL R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 144 removed outlier: 3.756A pdb=" N LEU R 115 " --> pdb=" O ALA R 111 " (cutoff:3.500A) Proline residue: R 117 - end of helix removed outlier: 3.727A pdb=" N ILE R 142 " --> pdb=" O ARG R 138 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN R 144 " --> pdb=" O GLN R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 169 removed outlier: 4.087A pdb=" N ALA R 155 " --> pdb=" O ASN R 151 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR R 156 " --> pdb=" O ASN R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 175 removed outlier: 3.817A pdb=" N LEU R 174 " --> pdb=" O SER R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 220 Processing helix chain 'R' and resid 220 through 239 removed outlier: 3.613A pdb=" N LEU R 224 " --> pdb=" O TYR R 220 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N CYS R 225 " --> pdb=" O PHE R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 240 through 245 Processing helix chain 'R' and resid 254 through 276 removed outlier: 3.685A pdb=" N ARG R 260 " --> pdb=" O SER R 256 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TRP R 276 " --> pdb=" O PHE R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 276 through 289 Processing helix chain 'R' and resid 297 through 311 removed outlier: 3.816A pdb=" N LEU R 301 " --> pdb=" O ASN R 297 " (cutoff:3.500A) Processing helix chain 'R' and resid 311 through 321 Proline residue: R 317 - end of helix Processing helix chain 'L' and resid 21 through 32 Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.606A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 255 removed outlier: 4.803A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.821A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.135A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.021A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.994A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 33 Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.969A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 4.339A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.924A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 7.462A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.280A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.724A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.205A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.897A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.514A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.474A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.743A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.058A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR S 50 " --> pdb=" O TYR S 59 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.058A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.448A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1167 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: 2.55 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2919 1.35 - 1.47: 2284 1.47 - 1.60: 3935 1.60 - 1.72: 0 1.72 - 1.85: 96 Bond restraints: 9234 Sorted by residual: bond pdb=" N VAL B 71 " pdb=" CA VAL B 71 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.15e-02 7.56e+03 1.01e+01 bond pdb=" N ILE B 80 " pdb=" CA ILE B 80 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.93e+00 bond pdb=" N ARG B 150 " pdb=" CA ARG B 150 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.23e-02 6.61e+03 9.70e+00 bond pdb=" N VAL R 122 " pdb=" CA VAL R 122 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.80e+00 bond pdb=" N CYS B 149 " pdb=" CA CYS B 149 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.40e+00 ... (remaining 9229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 11846 1.33 - 2.66: 534 2.66 - 3.98: 99 3.98 - 5.31: 20 5.31 - 6.64: 7 Bond angle restraints: 12506 Sorted by residual: angle pdb=" N MET S 192 " pdb=" CA MET S 192 " pdb=" CB MET S 192 " ideal model delta sigma weight residual 114.17 109.67 4.50 1.14e+00 7.69e-01 1.56e+01 angle pdb=" N MET R 179 " pdb=" CA MET R 179 " pdb=" C MET R 179 " ideal model delta sigma weight residual 113.88 109.52 4.36 1.23e+00 6.61e-01 1.26e+01 angle pdb=" CA TRP B 339 " pdb=" C TRP B 339 " pdb=" O TRP B 339 " ideal model delta sigma weight residual 121.56 117.89 3.67 1.09e+00 8.42e-01 1.13e+01 angle pdb=" CA LEU A 36 " pdb=" C LEU A 36 " pdb=" O LEU A 36 " ideal model delta sigma weight residual 121.58 117.70 3.88 1.16e+00 7.43e-01 1.12e+01 angle pdb=" N GLY B 77 " pdb=" CA GLY B 77 " pdb=" C GLY B 77 " ideal model delta sigma weight residual 115.63 110.85 4.78 1.49e+00 4.50e-01 1.03e+01 ... (remaining 12501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.19: 4960 16.19 - 32.39: 424 32.39 - 48.58: 90 48.58 - 64.78: 11 64.78 - 80.97: 7 Dihedral angle restraints: 5492 sinusoidal: 2150 harmonic: 3342 Sorted by residual: dihedral pdb=" CB CYS R 113 " pdb=" SG CYS R 113 " pdb=" SG CYS R 198 " pdb=" CB CYS R 198 " ideal model delta sinusoidal sigma weight residual -86.00 -154.34 68.34 1 1.00e+01 1.00e-02 6.06e+01 dihedral pdb=" CA THR R 180 " pdb=" C THR R 180 " pdb=" N ASP R 181 " pdb=" CA ASP R 181 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA TYR S 101 " pdb=" C TYR S 101 " pdb=" N TYR S 102 " pdb=" CA TYR S 102 " ideal model delta harmonic sigma weight residual 180.00 162.03 17.97 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 5489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1148 0.054 - 0.108: 220 0.108 - 0.162: 41 0.162 - 0.216: 5 0.216 - 0.270: 2 Chirality restraints: 1416 Sorted by residual: chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA LEU A 36 " pdb=" N LEU A 36 " pdb=" C LEU A 36 " pdb=" CB LEU A 36 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE A 222 " pdb=" CA ILE A 222 " pdb=" CG1 ILE A 222 " pdb=" CG2 ILE A 222 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1413 not shown) Planarity restraints: 1583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO B 236 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 35 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO R 36 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO R 36 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 36 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE S 68 " 0.004 2.00e-02 2.50e+03 9.53e-03 1.59e+00 pdb=" CG PHE S 68 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE S 68 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE S 68 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE S 68 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE S 68 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE S 68 " -0.000 2.00e-02 2.50e+03 ... (remaining 1580 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1906 2.78 - 3.31: 8068 3.31 - 3.84: 13740 3.84 - 4.37: 15597 4.37 - 4.90: 28663 Nonbonded interactions: 67974 Sorted by model distance: nonbonded pdb=" OG SER A 293 " pdb=" OE1 GLU A 298 " model vdw 2.255 3.040 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.289 3.040 nonbonded pdb=" NH2 ARG B 256 " pdb=" OD2 ASP G 36 " model vdw 2.289 3.120 nonbonded pdb=" NE2 GLN G 18 " pdb=" OE2 GLU G 22 " model vdw 2.302 3.120 nonbonded pdb=" O THR B 34 " pdb=" NZ LYS B 301 " model vdw 2.325 3.120 ... (remaining 67969 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: 5.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.870 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 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 : 0.004 0.039 9234 Z= 0.257 Angle : 0.652 6.641 12506 Z= 0.384 Chirality : 0.046 0.270 1416 Planarity : 0.003 0.039 1583 Dihedral : 12.657 80.973 3323 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.12 (0.25), residues: 1126 helix: 2.00 (0.28), residues: 368 sheet: -0.33 (0.32), residues: 254 loop : -1.15 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.009 0.001 HIS B 142 PHE 0.019 0.001 PHE S 68 TYR 0.014 0.001 TYR S 59 ARG 0.006 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: R 103 MET cc_start: 0.7710 (mtm) cc_final: 0.7407 (mtt) REVERT: A 29 LYS cc_start: 0.7969 (tmtt) cc_final: 0.7730 (tttm) REVERT: B 312 ASP cc_start: 0.7539 (t70) cc_final: 0.7336 (t0) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2652 time to fit residues: 53.0753 Evaluate side-chains 125 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 102 optimal weight: 0.0020 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 316 ASN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9234 Z= 0.211 Angle : 0.563 6.592 12506 Z= 0.297 Chirality : 0.042 0.174 1416 Planarity : 0.004 0.038 1583 Dihedral : 4.246 26.588 1250 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.42 % Allowed : 7.70 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.26 (0.25), residues: 1126 helix: 2.09 (0.27), residues: 377 sheet: -0.28 (0.31), residues: 278 loop : -1.14 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 339 HIS 0.009 0.001 HIS B 142 PHE 0.014 0.001 PHE R 118 TYR 0.011 0.001 TYR S 173 ARG 0.003 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 0.989 Fit side-chains REVERT: R 103 MET cc_start: 0.7664 (mtm) cc_final: 0.7360 (mtt) REVERT: B 17 GLN cc_start: 0.7568 (tm-30) cc_final: 0.6422 (tt0) REVERT: B 188 MET cc_start: 0.8607 (mmt) cc_final: 0.8162 (mmt) REVERT: B 215 GLU cc_start: 0.7641 (mp0) cc_final: 0.7413 (mp0) REVERT: B 312 ASP cc_start: 0.7568 (t70) cc_final: 0.7298 (t0) REVERT: G 58 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7546 (mm-30) outliers start: 14 outliers final: 9 residues processed: 133 average time/residue: 0.2740 time to fit residues: 47.4769 Evaluate side-chains 125 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 275 CYS Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain R residue 311 ILE Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9234 Z= 0.228 Angle : 0.555 7.344 12506 Z= 0.292 Chirality : 0.042 0.161 1416 Planarity : 0.003 0.038 1583 Dihedral : 4.085 17.957 1250 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.93 % Allowed : 11.25 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.32 (0.25), residues: 1126 helix: 2.13 (0.27), residues: 380 sheet: -0.14 (0.31), residues: 278 loop : -1.18 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.010 0.001 HIS B 142 PHE 0.014 0.001 PHE R 272 TYR 0.009 0.001 TYR S 175 ARG 0.005 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 0.926 Fit side-chains REVERT: R 103 MET cc_start: 0.7704 (mtm) cc_final: 0.7341 (mtt) REVERT: B 17 GLN cc_start: 0.7505 (tm-30) cc_final: 0.6407 (tt0) REVERT: B 23 LYS cc_start: 0.7970 (tmmt) cc_final: 0.7544 (tppt) REVERT: B 188 MET cc_start: 0.8596 (mmt) cc_final: 0.8155 (mmt) REVERT: B 285 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8116 (pt) REVERT: B 312 ASP cc_start: 0.7590 (t70) cc_final: 0.7299 (t0) REVERT: G 58 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7532 (mm-30) outliers start: 19 outliers final: 11 residues processed: 133 average time/residue: 0.2630 time to fit residues: 45.6846 Evaluate side-chains 130 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain R residue 315 VAL Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.4980 chunk 77 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 49 optimal weight: 0.0050 chunk 69 optimal weight: 0.3980 chunk 103 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 243 ASN R 316 ASN A 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9234 Z= 0.136 Angle : 0.480 7.598 12506 Z= 0.255 Chirality : 0.040 0.167 1416 Planarity : 0.003 0.035 1583 Dihedral : 3.768 17.045 1250 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.52 % Allowed : 14.08 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1126 helix: 2.26 (0.27), residues: 381 sheet: 0.04 (0.31), residues: 278 loop : -1.07 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.007 0.001 HIS B 142 PHE 0.010 0.001 PHE R 272 TYR 0.008 0.001 TYR S 102 ARG 0.006 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 1.026 Fit side-chains REVERT: R 103 MET cc_start: 0.7511 (mtm) cc_final: 0.7199 (mtt) REVERT: B 17 GLN cc_start: 0.7435 (tm-30) cc_final: 0.6450 (tt0) REVERT: B 23 LYS cc_start: 0.7920 (tmmt) cc_final: 0.7517 (tppt) REVERT: B 188 MET cc_start: 0.8566 (mmt) cc_final: 0.8214 (mmt) REVERT: B 312 ASP cc_start: 0.7515 (t70) cc_final: 0.7258 (t0) REVERT: G 58 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7504 (mm-30) outliers start: 15 outliers final: 6 residues processed: 129 average time/residue: 0.2633 time to fit residues: 44.4629 Evaluate side-chains 122 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 243 ASN ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9234 Z= 0.296 Angle : 0.581 8.722 12506 Z= 0.306 Chirality : 0.043 0.145 1416 Planarity : 0.004 0.038 1583 Dihedral : 4.125 17.396 1250 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.53 % Allowed : 14.49 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1126 helix: 2.15 (0.28), residues: 381 sheet: 0.02 (0.31), residues: 282 loop : -1.16 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.011 0.002 HIS B 142 PHE 0.016 0.002 PHE R 118 TYR 0.024 0.001 TYR S 190 ARG 0.006 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 1.255 Fit side-chains REVERT: R 103 MET cc_start: 0.7728 (mtm) cc_final: 0.7357 (mtt) REVERT: B 23 LYS cc_start: 0.7999 (tmmt) cc_final: 0.7584 (tppt) REVERT: B 285 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8107 (pt) REVERT: B 312 ASP cc_start: 0.7590 (t70) cc_final: 0.7292 (t0) REVERT: G 58 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7540 (mm-30) outliers start: 25 outliers final: 17 residues processed: 138 average time/residue: 0.2520 time to fit residues: 46.5895 Evaluate side-chains 135 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 315 VAL Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 chunk 109 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 57 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 243 ASN ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9234 Z= 0.177 Angle : 0.508 8.623 12506 Z= 0.269 Chirality : 0.041 0.182 1416 Planarity : 0.003 0.037 1583 Dihedral : 3.914 17.270 1250 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.13 % Allowed : 15.20 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1126 helix: 2.26 (0.28), residues: 380 sheet: 0.12 (0.31), residues: 280 loop : -1.12 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.008 0.001 HIS B 142 PHE 0.012 0.001 PHE R 272 TYR 0.021 0.001 TYR S 190 ARG 0.006 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 1.025 Fit side-chains REVERT: R 103 MET cc_start: 0.7613 (mtm) cc_final: 0.7241 (mtt) REVERT: L 30 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6861 (mp) REVERT: A 38 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7980 (mp) REVERT: B 17 GLN cc_start: 0.7448 (tm-30) cc_final: 0.6389 (tt0) REVERT: B 312 ASP cc_start: 0.7544 (t70) cc_final: 0.7275 (t0) REVERT: G 58 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7508 (mm-30) outliers start: 21 outliers final: 10 residues processed: 129 average time/residue: 0.2624 time to fit residues: 44.8529 Evaluate side-chains 127 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 243 ASN ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9234 Z= 0.234 Angle : 0.542 6.388 12506 Z= 0.287 Chirality : 0.042 0.155 1416 Planarity : 0.003 0.037 1583 Dihedral : 4.013 17.289 1250 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.74 % Allowed : 15.20 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.45 (0.25), residues: 1126 helix: 2.09 (0.28), residues: 387 sheet: 0.13 (0.31), residues: 282 loop : -1.18 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.008 0.001 HIS B 142 PHE 0.013 0.001 PHE R 118 TYR 0.019 0.001 TYR S 190 ARG 0.007 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 0.973 Fit side-chains REVERT: R 103 MET cc_start: 0.7687 (mtm) cc_final: 0.7322 (mtt) REVERT: L 30 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6873 (mp) REVERT: A 38 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8037 (mp) REVERT: A 276 GLU cc_start: 0.6670 (pm20) cc_final: 0.6422 (pm20) REVERT: B 17 GLN cc_start: 0.7483 (tm-30) cc_final: 0.6403 (tt0) REVERT: B 285 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8107 (pt) REVERT: B 312 ASP cc_start: 0.7555 (t70) cc_final: 0.7261 (t0) REVERT: G 58 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7519 (mm-30) outliers start: 27 outliers final: 20 residues processed: 136 average time/residue: 0.2645 time to fit residues: 48.1290 Evaluate side-chains 136 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 275 CYS Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 10 optimal weight: 0.0970 chunk 85 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 243 ASN ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9234 Z= 0.238 Angle : 0.543 6.673 12506 Z= 0.287 Chirality : 0.042 0.205 1416 Planarity : 0.003 0.037 1583 Dihedral : 4.043 17.267 1250 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.94 % Allowed : 15.10 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.43 (0.25), residues: 1126 helix: 2.05 (0.28), residues: 387 sheet: 0.18 (0.31), residues: 282 loop : -1.21 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.007 0.001 HIS B 142 PHE 0.013 0.001 PHE R 118 TYR 0.019 0.001 TYR S 190 ARG 0.007 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 1.004 Fit side-chains REVERT: R 103 MET cc_start: 0.7714 (mtm) cc_final: 0.7336 (mtt) REVERT: R 219 GLN cc_start: 0.7621 (tt0) cc_final: 0.7401 (tt0) REVERT: L 30 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6866 (mp) REVERT: B 17 GLN cc_start: 0.7558 (tm-30) cc_final: 0.6533 (tt0) REVERT: B 36 ASN cc_start: 0.8147 (m-40) cc_final: 0.7926 (m-40) REVERT: B 285 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8078 (pt) REVERT: B 312 ASP cc_start: 0.7554 (t70) cc_final: 0.7196 (t0) REVERT: G 58 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7513 (mm-30) outliers start: 29 outliers final: 24 residues processed: 138 average time/residue: 0.2443 time to fit residues: 44.9453 Evaluate side-chains 141 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 91 optimal weight: 2.9990 chunk 95 optimal weight: 0.0030 chunk 66 optimal weight: 0.3980 chunk 107 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 243 ASN ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9234 Z= 0.177 Angle : 0.510 6.512 12506 Z= 0.270 Chirality : 0.041 0.160 1416 Planarity : 0.003 0.036 1583 Dihedral : 3.880 17.171 1250 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.84 % Allowed : 15.70 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.53 (0.25), residues: 1126 helix: 2.11 (0.28), residues: 387 sheet: 0.27 (0.31), residues: 280 loop : -1.15 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.005 0.001 HIS B 142 PHE 0.012 0.001 PHE R 272 TYR 0.019 0.001 TYR S 190 ARG 0.007 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 121 time to evaluate : 0.944 Fit side-chains REVERT: R 103 MET cc_start: 0.7642 (mtm) cc_final: 0.7285 (mtt) REVERT: R 142 ILE cc_start: 0.6731 (OUTLIER) cc_final: 0.6070 (tp) REVERT: R 219 GLN cc_start: 0.7554 (tt0) cc_final: 0.7341 (tt0) REVERT: L 30 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6849 (mp) REVERT: B 17 GLN cc_start: 0.7560 (tm-30) cc_final: 0.6570 (tt0) REVERT: B 285 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8067 (pt) REVERT: B 312 ASP cc_start: 0.7519 (t70) cc_final: 0.7168 (t0) REVERT: G 58 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7493 (mm-30) outliers start: 28 outliers final: 21 residues processed: 141 average time/residue: 0.2540 time to fit residues: 47.6871 Evaluate side-chains 141 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 275 CYS Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 71 optimal weight: 0.0970 chunk 95 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 243 ASN ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9234 Z= 0.183 Angle : 0.523 7.010 12506 Z= 0.276 Chirality : 0.041 0.174 1416 Planarity : 0.003 0.036 1583 Dihedral : 3.855 17.155 1250 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.53 % Allowed : 16.11 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.56 (0.25), residues: 1126 helix: 2.13 (0.28), residues: 387 sheet: 0.32 (0.31), residues: 280 loop : -1.15 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.005 0.001 HIS B 142 PHE 0.012 0.001 PHE R 272 TYR 0.018 0.001 TYR S 190 ARG 0.007 0.000 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 1.027 Fit side-chains REVERT: R 103 MET cc_start: 0.7626 (mtm) cc_final: 0.7254 (mtt) REVERT: R 142 ILE cc_start: 0.6674 (OUTLIER) cc_final: 0.6033 (tp) REVERT: R 219 GLN cc_start: 0.7559 (tt0) cc_final: 0.7347 (tt0) REVERT: L 30 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6871 (mp) REVERT: B 17 GLN cc_start: 0.7550 (tm-30) cc_final: 0.6563 (tt0) REVERT: B 285 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8073 (pt) REVERT: B 312 ASP cc_start: 0.7518 (t70) cc_final: 0.7170 (t0) REVERT: G 58 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7494 (mm-30) outliers start: 25 outliers final: 21 residues processed: 136 average time/residue: 0.2411 time to fit residues: 43.9137 Evaluate side-chains 140 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.0534 > 50: distance: 35 - 40: 21.985 distance: 40 - 41: 24.251 distance: 41 - 42: 22.022 distance: 41 - 44: 54.464 distance: 42 - 48: 34.205 distance: 44 - 45: 12.615 distance: 45 - 46: 7.240 distance: 45 - 47: 11.924 distance: 48 - 49: 13.653 distance: 48 - 54: 56.312 distance: 49 - 50: 5.502 distance: 49 - 52: 34.872 distance: 50 - 51: 3.675 distance: 50 - 55: 15.475 distance: 52 - 53: 3.771 distance: 53 - 54: 56.355 distance: 55 - 56: 13.245 distance: 56 - 57: 21.028 distance: 56 - 59: 11.711 distance: 57 - 58: 42.940 distance: 57 - 66: 14.334 distance: 61 - 62: 13.590 distance: 62 - 63: 18.045 distance: 63 - 64: 29.727 distance: 63 - 65: 27.659 distance: 66 - 67: 21.954 distance: 67 - 68: 7.363 distance: 68 - 69: 21.163 distance: 68 - 70: 27.548 distance: 70 - 71: 7.411 distance: 71 - 72: 10.457 distance: 71 - 74: 13.574 distance: 72 - 73: 43.920 distance: 72 - 84: 34.385 distance: 74 - 75: 9.578 distance: 75 - 76: 26.601 distance: 75 - 77: 16.887 distance: 76 - 78: 3.973 distance: 77 - 79: 18.832 distance: 77 - 80: 26.215 distance: 78 - 79: 13.064 distance: 79 - 81: 27.507 distance: 80 - 82: 34.272 distance: 84 - 85: 11.847 distance: 85 - 86: 44.610 distance: 85 - 88: 38.255 distance: 86 - 87: 17.632 distance: 86 - 95: 8.150 distance: 88 - 89: 8.921 distance: 89 - 90: 37.011 distance: 90 - 91: 27.978 distance: 91 - 92: 19.358 distance: 92 - 94: 3.136 distance: 95 - 96: 36.877 distance: 95 - 101: 18.443 distance: 96 - 97: 40.765 distance: 96 - 99: 8.367 distance: 97 - 98: 18.165 distance: 97 - 102: 30.429 distance: 99 - 100: 36.216 distance: 100 - 101: 33.960 distance: 102 - 103: 8.098 distance: 103 - 104: 27.839 distance: 103 - 106: 22.874 distance: 104 - 105: 21.316 distance: 104 - 110: 3.500 distance: 106 - 107: 18.725 distance: 107 - 108: 36.746 distance: 107 - 109: 35.439 distance: 110 - 111: 11.067 distance: 111 - 112: 9.549 distance: 111 - 114: 9.576 distance: 112 - 113: 12.583 distance: 112 - 118: 24.171 distance: 114 - 115: 13.889 distance: 115 - 116: 36.427 distance: 115 - 117: 26.176 distance: 118 - 119: 7.423 distance: 119 - 120: 16.296 distance: 119 - 122: 7.707 distance: 120 - 121: 11.693 distance: 120 - 129: 8.680 distance: 121 - 155: 14.439 distance: 122 - 123: 10.854 distance: 123 - 124: 8.595 distance: 124 - 125: 3.259 distance: 125 - 126: 15.916 distance: 126 - 128: 15.354