Starting phenix.real_space_refine on Mon Mar 11 08:13:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gdb_29945/03_2024/8gdb_29945_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gdb_29945/03_2024/8gdb_29945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gdb_29945/03_2024/8gdb_29945.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gdb_29945/03_2024/8gdb_29945.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gdb_29945/03_2024/8gdb_29945_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gdb_29945/03_2024/8gdb_29945_neut_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 46 5.16 5 C 4856 2.51 5 N 1336 2.21 5 O 1374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 344": "OE1" <-> "OE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N ARG 67": "NH1" <-> "NH2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "R GLU 116": "OE1" <-> "OE2" Residue "R PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 162": "NH1" <-> "NH2" Residue "R ARG 212": "NH1" <-> "NH2" Residue "R ARG 220": "NH1" <-> "NH2" Residue "R GLU 267": "OE1" <-> "OE2" Residue "R ARG 333": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7612 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1751 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 8, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 115 Chain: "B" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2475 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 11, 'ASN%COO:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 105 Chain: "G" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 381 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "N" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 904 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2076 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 12, 'TRANS': 270} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'P2E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.60, per 1000 atoms: 0.60 Number of scatterers: 7612 At special positions: 0 Unit cell: (99.36, 99.36, 124.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1374 8.00 N 1336 7.00 C 4856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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: 2.94 Conformation dependent library (CDL) restraints added in 1.5 seconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 10 sheets defined 36.2% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.781A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.675A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 335 through 349 removed outlier: 3.536A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 390 removed outlier: 3.841A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 6 through 22 Processing helix chain 'G' and resid 30 through 43 removed outlier: 3.605A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 22 through 43 removed outlier: 3.550A pdb=" N ALA R 38 " --> pdb=" O GLY R 34 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE R 39 " --> pdb=" O ASN R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 49 No H-bonds generated for 'chain 'R' and resid 47 through 49' Processing helix chain 'R' and resid 55 through 81 Proline residue: R 74 - end of helix removed outlier: 3.633A pdb=" N ILE R 77 " --> pdb=" O SER R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 122 removed outlier: 3.668A pdb=" N CYS R 92 " --> pdb=" O GLY R 88 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU R 93 " --> pdb=" O GLN R 89 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR R 94 " --> pdb=" O PRO R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 130 Processing helix chain 'R' and resid 133 through 152 Processing helix chain 'R' and resid 180 through 220 Processing helix chain 'R' and resid 268 through 297 Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 310 through 329 Proline residue: R 322 - end of helix Proline residue: R 326 - end of helix removed outlier: 3.984A pdb=" N TYR R 329 " --> pdb=" O ASP R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 334 through 343 removed outlier: 4.385A pdb=" N LYS R 339 " --> pdb=" O THR R 335 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 359 through 362 removed outlier: 7.167A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP A 223 " --> pdb=" O PHE A 208 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.717A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.860A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.684A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.072A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.760A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.795A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.644A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.514A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.934A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 1044 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: 2.14 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1419 1.33 - 1.45: 1969 1.45 - 1.57: 4314 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 7764 Sorted by residual: bond pdb=" C1 P2E R 501 " pdb=" O2 P2E R 501 " ideal model delta sigma weight residual 1.250 1.306 -0.056 2.00e-02 2.50e+03 7.70e+00 bond pdb=" C1 P2E R 501 " pdb=" C2 P2E R 501 " ideal model delta sigma weight residual 1.539 1.499 0.040 2.00e-02 2.50e+03 3.94e+00 bond pdb=" C1 P2E R 501 " pdb=" O1 P2E R 501 " ideal model delta sigma weight residual 1.247 1.211 0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" C ILE R 286 " pdb=" N PRO R 287 " ideal model delta sigma weight residual 1.335 1.359 -0.023 1.36e-02 5.41e+03 2.89e+00 bond pdb=" N PRO R 24 " pdb=" CD PRO R 24 " ideal model delta sigma weight residual 1.473 1.495 -0.022 1.40e-02 5.10e+03 2.50e+00 ... (remaining 7759 not shown) Histogram of bond angle deviations from ideal: 97.61 - 104.92: 100 104.92 - 112.22: 3863 112.22 - 119.52: 2511 119.52 - 126.82: 4013 126.82 - 134.12: 97 Bond angle restraints: 10584 Sorted by residual: angle pdb=" C TYR A 360 " pdb=" N PRO A 361 " pdb=" CA PRO A 361 " ideal model delta sigma weight residual 119.76 125.82 -6.06 1.00e+00 1.00e+00 3.68e+01 angle pdb=" N GLN R 84 " pdb=" CA GLN R 84 " pdb=" C GLN R 84 " ideal model delta sigma weight residual 109.59 116.44 -6.85 1.47e+00 4.63e-01 2.17e+01 angle pdb=" N VAL R 75 " pdb=" CA VAL R 75 " pdb=" C VAL R 75 " ideal model delta sigma weight residual 110.30 114.06 -3.76 9.70e-01 1.06e+00 1.50e+01 angle pdb=" C GLU A 327 " pdb=" N PRO A 328 " pdb=" CA PRO A 328 " ideal model delta sigma weight residual 118.97 115.28 3.69 1.04e+00 9.25e-01 1.26e+01 angle pdb=" N LEU R 71 " pdb=" CA LEU R 71 " pdb=" C LEU R 71 " ideal model delta sigma weight residual 111.40 115.64 -4.24 1.22e+00 6.72e-01 1.21e+01 ... (remaining 10579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.78: 4234 19.78 - 39.55: 279 39.55 - 59.33: 36 59.33 - 79.10: 15 79.10 - 98.88: 5 Dihedral angle restraints: 4569 sinusoidal: 1557 harmonic: 3012 Sorted by residual: dihedral pdb=" CA LYS N 33 " pdb=" C LYS N 33 " pdb=" N MET N 34 " pdb=" CA MET N 34 " ideal model delta harmonic sigma weight residual 180.00 150.11 29.89 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 155.87 24.13 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA LEU R 331 " pdb=" C LEU R 331 " pdb=" N LEU R 332 " pdb=" CA LEU R 332 " ideal model delta harmonic sigma weight residual 180.00 159.56 20.44 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 4566 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 848 0.045 - 0.090: 280 0.090 - 0.136: 97 0.136 - 0.181: 17 0.181 - 0.226: 7 Chirality restraints: 1249 Sorted by residual: chirality pdb=" CB VAL R 320 " pdb=" CA VAL R 320 " pdb=" CG1 VAL R 320 " pdb=" CG2 VAL R 320 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C8 P2E R 501 " pdb=" C12 P2E R 501 " pdb=" C7 P2E R 501 " pdb=" C9 P2E R 501 " both_signs ideal model delta sigma weight residual False -2.53 -2.75 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA TYR B 59 " pdb=" N TYR B 59 " pdb=" C TYR B 59 " pdb=" CB TYR B 59 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1246 not shown) Planarity restraints: 1352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP R 325 " 0.043 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO R 326 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO R 326 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 326 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 23 " -0.043 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO R 24 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO R 24 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 24 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.041 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO B 236 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.035 5.00e-02 4.00e+02 ... (remaining 1349 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1648 2.78 - 3.31: 6653 3.31 - 3.84: 12082 3.84 - 4.37: 13821 4.37 - 4.90: 25192 Nonbonded interactions: 59396 Sorted by model distance: nonbonded pdb=" OE2 GLU A 230 " pdb=" NH1 ARG A 232 " model vdw 2.255 2.520 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.288 2.440 nonbonded pdb=" OG1 THR R 64 " pdb=" OH TYR R 144 " model vdw 2.311 2.440 nonbonded pdb=" OD1 ASN A 292 " pdb=" OG1 THR A 364 " model vdw 2.316 2.440 nonbonded pdb=" O LEU R 67 " pdb=" CD1 LEU R 71 " model vdw 2.319 3.460 ... (remaining 59391 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 3.230 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 23.970 Find NCS groups from input model: 0.210 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7764 Z= 0.296 Angle : 0.796 8.527 10584 Z= 0.467 Chirality : 0.052 0.226 1249 Planarity : 0.006 0.064 1352 Dihedral : 14.282 98.876 2615 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.28 % Allowed : 1.11 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1021 helix: 1.06 (0.26), residues: 379 sheet: -0.12 (0.35), residues: 229 loop : -1.79 (0.27), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.007 0.001 HIS A 357 PHE 0.017 0.002 PHE B 151 TYR 0.025 0.002 TYR N 60 ARG 0.010 0.001 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 0.909 Fit side-chains REVERT: A 320 THR cc_start: 0.8766 (t) cc_final: 0.8446 (m) outliers start: 2 outliers final: 2 residues processed: 132 average time/residue: 0.2269 time to fit residues: 39.4670 Evaluate side-chains 110 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 333 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 35 GLN A 218 ASN A 294 GLN B 175 GLN R 216 GLN R 269 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 7764 Z= 0.399 Angle : 0.632 6.187 10584 Z= 0.338 Chirality : 0.047 0.159 1249 Planarity : 0.005 0.050 1352 Dihedral : 7.919 61.940 1150 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.25 % Allowed : 7.21 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1021 helix: 1.92 (0.27), residues: 375 sheet: -0.19 (0.34), residues: 235 loop : -1.60 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP R 174 HIS 0.008 0.002 HIS A 220 PHE 0.021 0.002 PHE B 151 TYR 0.013 0.002 TYR N 95 ARG 0.004 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 0.945 Fit side-chains REVERT: B 78 LYS cc_start: 0.9004 (tppt) cc_final: 0.8719 (tptt) outliers start: 9 outliers final: 6 residues processed: 110 average time/residue: 0.2428 time to fit residues: 34.9454 Evaluate side-chains 109 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 319 SER Chi-restraints excluded: chain R residue 331 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 35 GLN A 279 ASN B 175 GLN R 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7764 Z= 0.203 Angle : 0.519 5.301 10584 Z= 0.276 Chirality : 0.042 0.142 1249 Planarity : 0.004 0.047 1352 Dihedral : 6.605 58.687 1145 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.25 % Allowed : 10.68 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.27), residues: 1021 helix: 2.27 (0.27), residues: 384 sheet: -0.13 (0.34), residues: 230 loop : -1.48 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE B 151 TYR 0.011 0.001 TYR R 130 ARG 0.003 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 0.794 Fit side-chains REVERT: B 78 LYS cc_start: 0.8994 (tppt) cc_final: 0.8450 (tptt) outliers start: 9 outliers final: 5 residues processed: 110 average time/residue: 0.2394 time to fit residues: 34.2457 Evaluate side-chains 105 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 319 SER Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 331 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 0.0980 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 0.1980 chunk 92 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 48 optimal weight: 0.1980 chunk 87 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7764 Z= 0.121 Angle : 0.456 5.351 10584 Z= 0.242 Chirality : 0.040 0.142 1249 Planarity : 0.003 0.045 1352 Dihedral : 5.711 56.125 1145 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.11 % Allowed : 11.79 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.27), residues: 1021 helix: 2.61 (0.27), residues: 384 sheet: -0.19 (0.34), residues: 240 loop : -1.25 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 85 HIS 0.004 0.001 HIS A 357 PHE 0.010 0.001 PHE R 102 TYR 0.009 0.001 TYR R 130 ARG 0.002 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 0.866 Fit side-chains REVERT: B 78 LYS cc_start: 0.9018 (tppt) cc_final: 0.8441 (tptt) REVERT: N 38 ARG cc_start: 0.8639 (ptt180) cc_final: 0.8286 (ptt-90) REVERT: R 116 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8236 (tm-30) outliers start: 8 outliers final: 6 residues processed: 113 average time/residue: 0.2430 time to fit residues: 35.3278 Evaluate side-chains 118 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 319 SER Chi-restraints excluded: chain R residue 320 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 72 optimal weight: 0.0770 chunk 40 optimal weight: 0.9980 chunk 83 optimal weight: 0.1980 chunk 67 optimal weight: 0.0770 chunk 0 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 35 GLN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7764 Z= 0.119 Angle : 0.452 6.528 10584 Z= 0.239 Chirality : 0.040 0.139 1249 Planarity : 0.003 0.044 1352 Dihedral : 5.387 46.921 1145 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.25 % Allowed : 12.07 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.27), residues: 1021 helix: 2.76 (0.27), residues: 384 sheet: -0.08 (0.34), residues: 238 loop : -1.19 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE R 102 TYR 0.008 0.001 TYR R 130 ARG 0.003 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 0.881 Fit side-chains REVERT: A 386 MET cc_start: 0.8000 (ttm) cc_final: 0.7787 (ttp) REVERT: B 78 LYS cc_start: 0.9028 (tppt) cc_final: 0.8437 (tptt) outliers start: 9 outliers final: 5 residues processed: 109 average time/residue: 0.2459 time to fit residues: 34.5301 Evaluate side-chains 104 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 320 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.0980 chunk 19 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 97 optimal weight: 0.0870 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.0870 chunk 51 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7764 Z= 0.104 Angle : 0.429 5.356 10584 Z= 0.227 Chirality : 0.040 0.136 1249 Planarity : 0.003 0.043 1352 Dihedral : 5.256 53.762 1145 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.25 % Allowed : 12.48 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.27), residues: 1021 helix: 2.86 (0.27), residues: 384 sheet: -0.11 (0.34), residues: 240 loop : -1.14 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 85 HIS 0.003 0.000 HIS A 357 PHE 0.010 0.001 PHE R 102 TYR 0.007 0.001 TYR R 130 ARG 0.004 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 0.948 Fit side-chains REVERT: B 78 LYS cc_start: 0.9044 (tppt) cc_final: 0.8455 (tptt) REVERT: R 100 LEU cc_start: 0.8942 (mt) cc_final: 0.8719 (mt) outliers start: 9 outliers final: 7 residues processed: 112 average time/residue: 0.2405 time to fit residues: 35.0507 Evaluate side-chains 112 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 319 SER Chi-restraints excluded: chain R residue 332 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 35 GLN B 175 GLN ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7764 Z= 0.239 Angle : 0.507 6.253 10584 Z= 0.272 Chirality : 0.042 0.138 1249 Planarity : 0.003 0.043 1352 Dihedral : 5.348 45.069 1145 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.53 % Allowed : 13.31 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.27), residues: 1021 helix: 2.74 (0.27), residues: 384 sheet: 0.01 (0.34), residues: 238 loop : -1.22 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 339 HIS 0.006 0.001 HIS A 357 PHE 0.017 0.001 PHE B 151 TYR 0.011 0.001 TYR N 95 ARG 0.004 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 0.863 Fit side-chains REVERT: A 386 MET cc_start: 0.8047 (ttm) cc_final: 0.7819 (ttp) REVERT: B 78 LYS cc_start: 0.9013 (tppt) cc_final: 0.8490 (tptt) outliers start: 11 outliers final: 9 residues processed: 109 average time/residue: 0.2531 time to fit residues: 35.9105 Evaluate side-chains 113 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 319 SER Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 332 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 0.0870 chunk 76 optimal weight: 2.9990 chunk 88 optimal weight: 0.0970 chunk 93 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 35 GLN B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7764 Z= 0.164 Angle : 0.462 5.385 10584 Z= 0.248 Chirality : 0.041 0.138 1249 Planarity : 0.003 0.042 1352 Dihedral : 4.958 46.294 1145 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.53 % Allowed : 13.31 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.27), residues: 1021 helix: 2.81 (0.27), residues: 383 sheet: -0.08 (0.34), residues: 242 loop : -1.20 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE B 151 TYR 0.013 0.001 TYR N 60 ARG 0.003 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 0.911 Fit side-chains REVERT: A 386 MET cc_start: 0.8039 (ttm) cc_final: 0.7816 (ttp) REVERT: B 78 LYS cc_start: 0.9017 (tppt) cc_final: 0.8487 (tptt) outliers start: 11 outliers final: 7 residues processed: 108 average time/residue: 0.2362 time to fit residues: 33.2517 Evaluate side-chains 107 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 319 SER Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 332 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN B 175 GLN R 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7764 Z= 0.178 Angle : 0.472 7.289 10584 Z= 0.253 Chirality : 0.041 0.139 1249 Planarity : 0.003 0.042 1352 Dihedral : 5.048 49.956 1145 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.25 % Allowed : 13.59 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.27), residues: 1021 helix: 2.82 (0.27), residues: 382 sheet: -0.01 (0.34), residues: 240 loop : -1.23 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.013 0.001 PHE B 151 TYR 0.014 0.001 TYR N 60 ARG 0.003 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 0.899 Fit side-chains REVERT: A 386 MET cc_start: 0.8050 (ttm) cc_final: 0.7826 (ttp) REVERT: B 78 LYS cc_start: 0.9013 (tppt) cc_final: 0.8488 (tptt) REVERT: G 52 THR cc_start: 0.7455 (OUTLIER) cc_final: 0.7209 (p) outliers start: 9 outliers final: 8 residues processed: 109 average time/residue: 0.2415 time to fit residues: 34.1423 Evaluate side-chains 109 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 319 SER Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 61 optimal weight: 4.9990 chunk 49 optimal weight: 0.1980 chunk 63 optimal weight: 0.2980 chunk 85 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 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 14 ASN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7764 Z= 0.128 Angle : 0.442 7.173 10584 Z= 0.236 Chirality : 0.040 0.137 1249 Planarity : 0.003 0.043 1352 Dihedral : 4.909 55.432 1145 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.11 % Allowed : 13.87 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.27), residues: 1021 helix: 2.91 (0.27), residues: 382 sheet: -0.01 (0.34), residues: 241 loop : -1.18 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 85 HIS 0.004 0.001 HIS A 357 PHE 0.010 0.001 PHE R 102 TYR 0.014 0.001 TYR N 60 ARG 0.004 0.000 ARG R 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 0.816 Fit side-chains REVERT: A 386 MET cc_start: 0.8016 (ttm) cc_final: 0.7801 (ttp) REVERT: B 78 LYS cc_start: 0.9042 (tppt) cc_final: 0.8475 (tptt) REVERT: G 52 THR cc_start: 0.7354 (OUTLIER) cc_final: 0.7145 (p) outliers start: 8 outliers final: 6 residues processed: 109 average time/residue: 0.2444 time to fit residues: 34.3319 Evaluate side-chains 108 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 320 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN B 175 GLN ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.116589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.091200 restraints weight = 10698.566| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.00 r_work: 0.2845 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7764 Z= 0.205 Angle : 0.485 7.119 10584 Z= 0.260 Chirality : 0.041 0.140 1249 Planarity : 0.003 0.042 1352 Dihedral : 5.107 56.666 1145 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.97 % Allowed : 14.15 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.27), residues: 1021 helix: 2.85 (0.27), residues: 382 sheet: 0.02 (0.34), residues: 240 loop : -1.23 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 85 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE B 151 TYR 0.014 0.001 TYR N 60 ARG 0.009 0.000 ARG R 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1963.29 seconds wall clock time: 36 minutes 6.67 seconds (2166.67 seconds total)