Starting phenix.real_space_refine (version: dev) on Tue Dec 13 01:03:40 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9s_6272/12_2022/3j9s_6272_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9s_6272/12_2022/3j9s_6272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9s_6272/12_2022/3j9s_6272.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9s_6272/12_2022/3j9s_6272.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9s_6272/12_2022/3j9s_6272_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9s_6272/12_2022/3j9s_6272_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "C GLU 134": "OE1" <-> "OE2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D GLU 230": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 13084 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3271 Unusual residues: {' CA': 2, ' CL': 1, ' ZN': 1, 'ACE': 1} Inner-chain residues flagged as termini: ['pdbres="LYS B 397 "'] Classifications: {'peptide': 397, 'undetermined': 5, 'water': 105} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 376, None: 109} Not linked: pdbres="LYS B 397 " pdbres=" ZN B 501 " Not linked: pdbres=" ZN B 501 " pdbres=" CL B 502 " Not linked: pdbres=" CL B 502 " pdbres=" CA B 503 " Not linked: pdbres=" CA B 503 " pdbres=" CA B 504 " Not linked: pdbres=" CA B 504 " pdbres="HOH B 601 " ... (remaining 104 not shown) Chain: "A" Number of atoms: 3271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3271 Unusual residues: {' CA': 2, ' CL': 1, ' ZN': 1, 'ACE': 1} Inner-chain residues flagged as termini: ['pdbres="LYS A 397 "'] Classifications: {'peptide': 397, 'undetermined': 5, 'water': 105} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 376, None: 109} Not linked: pdbres="LYS A 397 " pdbres=" ZN A 501 " Not linked: pdbres=" ZN A 501 " pdbres=" CL A 502 " Not linked: pdbres=" CL A 502 " pdbres=" CA A 503 " Not linked: pdbres=" CA A 503 " pdbres=" CA A 504 " Not linked: pdbres=" CA A 504 " pdbres="HOH A 601 " ... (remaining 104 not shown) Chain: "C" Number of atoms: 3271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3271 Unusual residues: {' CA': 2, ' CL': 1, ' ZN': 1, 'ACE': 1} Inner-chain residues flagged as termini: ['pdbres="LYS C 397 "'] Classifications: {'peptide': 397, 'undetermined': 5, 'water': 105} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 376, None: 109} Not linked: pdbres="LYS C 397 " pdbres=" ZN C 501 " Not linked: pdbres=" ZN C 501 " pdbres=" CL C 502 " Not linked: pdbres=" CL C 502 " pdbres=" CA C 503 " Not linked: pdbres=" CA C 503 " pdbres=" CA C 504 " Not linked: pdbres=" CA C 504 " pdbres="HOH C 601 " ... (remaining 104 not shown) Chain: "D" Number of atoms: 3271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3271 Unusual residues: {' CA': 2, ' CL': 1, ' ZN': 1, 'ACE': 1} Inner-chain residues flagged as termini: ['pdbres="LYS D 397 "'] Classifications: {'peptide': 397, 'undetermined': 5, 'water': 105} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 376, None: 109} Not linked: pdbres="LYS D 397 " pdbres=" ZN D 501 " Not linked: pdbres=" ZN D 501 " pdbres=" CL D 502 " Not linked: pdbres=" CL D 502 " pdbres=" CA D 503 " Not linked: pdbres=" CA D 503 " pdbres=" CA D 504 " Not linked: pdbres=" CA D 504 " pdbres="HOH D 601 " ... (remaining 104 not shown) Time building chain proxies: 7.87, per 1000 atoms: 0.60 Number of scatterers: 13084 At special positions: 0 Unit cell: (91.047, 84.909, 106.392, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 8 19.99 Cl 4 17.00 S 60 16.00 O 2808 8.00 N 2184 7.00 C 8016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.87 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS D 153 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 153 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS A 153 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS C 153 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 153 " 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 20 sheets defined 32.7% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'B' and resid 2 through 17 Processing helix chain 'B' and resid 24 through 41 removed outlier: 5.013A pdb=" N ASP B 29 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LEU B 30 " --> pdb=" O ASN B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 100 removed outlier: 3.736A pdb=" N THR B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.867A pdb=" N ARG B 126 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 302 through 307 removed outlier: 3.637A pdb=" N LEU B 307 " --> pdb=" O ALA B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 376 through 395 removed outlier: 3.995A pdb=" N LEU B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 17 Processing helix chain 'A' and resid 24 through 41 removed outlier: 5.012A pdb=" N ASP A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LEU A 30 " --> pdb=" O ASN A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 100 removed outlier: 3.735A pdb=" N THR A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 119 Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.867A pdb=" N ARG A 126 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 302 through 307 removed outlier: 3.636A pdb=" N LEU A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 352 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 376 through 395 removed outlier: 3.994A pdb=" N LEU A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 17 Processing helix chain 'C' and resid 24 through 41 removed outlier: 5.012A pdb=" N ASP C 29 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU C 30 " --> pdb=" O ASN C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 100 removed outlier: 3.736A pdb=" N THR C 84 " --> pdb=" O THR C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 119 Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.867A pdb=" N ARG C 126 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 143 Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 302 through 307 removed outlier: 3.637A pdb=" N LEU C 307 " --> pdb=" O ALA C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 352 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'C' and resid 376 through 395 removed outlier: 3.994A pdb=" N LEU C 395 " --> pdb=" O ILE C 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 17 Processing helix chain 'D' and resid 24 through 41 removed outlier: 5.012A pdb=" N ASP D 29 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU D 30 " --> pdb=" O ASN D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 100 removed outlier: 3.735A pdb=" N THR D 84 " --> pdb=" O THR D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 123 through 127 removed outlier: 3.866A pdb=" N ARG D 126 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 143 Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 302 through 307 removed outlier: 3.637A pdb=" N LEU D 307 " --> pdb=" O ALA D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 352 Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 376 through 395 removed outlier: 3.994A pdb=" N LEU D 395 " --> pdb=" O ILE D 391 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 45 through 48 Processing sheet with id= B, first strand: chain 'B' and resid 150 through 153 removed outlier: 6.526A pdb=" N THR B 222 " --> pdb=" O GLU B 327 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 251 through 253 removed outlier: 5.867A pdb=" N HIS B 317 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET B 177 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N THR B 179 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TRP B 181 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N PHE B 164 " --> pdb=" O TRP B 181 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASN B 183 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ALA B 162 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 205 through 213 removed outlier: 6.227A pdb=" N LEU B 265 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ILE B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 236 through 239 Processing sheet with id= F, first strand: chain 'A' and resid 45 through 48 Processing sheet with id= G, first strand: chain 'A' and resid 150 through 153 removed outlier: 6.526A pdb=" N THR A 222 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 251 through 253 removed outlier: 5.867A pdb=" N HIS A 317 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET A 177 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N THR A 179 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU A 166 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TRP A 181 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N PHE A 164 " --> pdb=" O TRP A 181 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASN A 183 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ALA A 162 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 205 through 213 removed outlier: 6.227A pdb=" N LEU A 265 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ILE A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 236 through 239 Processing sheet with id= K, first strand: chain 'C' and resid 45 through 48 Processing sheet with id= L, first strand: chain 'C' and resid 150 through 153 removed outlier: 6.527A pdb=" N THR C 222 " --> pdb=" O GLU C 327 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 251 through 253 removed outlier: 5.867A pdb=" N HIS C 317 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET C 177 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR C 179 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TRP C 181 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N PHE C 164 " --> pdb=" O TRP C 181 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASN C 183 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ALA C 162 " --> pdb=" O ASN C 183 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 205 through 213 removed outlier: 6.227A pdb=" N LEU C 265 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ILE C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 236 through 239 Processing sheet with id= P, first strand: chain 'D' and resid 45 through 48 Processing sheet with id= Q, first strand: chain 'D' and resid 150 through 153 removed outlier: 6.526A pdb=" N THR D 222 " --> pdb=" O GLU D 327 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 251 through 253 removed outlier: 5.867A pdb=" N HIS D 317 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET D 177 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N THR D 179 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU D 166 " --> pdb=" O THR D 179 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TRP D 181 " --> pdb=" O PHE D 164 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N PHE D 164 " --> pdb=" O TRP D 181 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASN D 183 " --> pdb=" O ALA D 162 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ALA D 162 " --> pdb=" O ASN D 183 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 205 through 213 removed outlier: 6.228A pdb=" N LEU D 265 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ILE D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 236 through 239 548 hydrogen bonds defined for protein. 1536 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: 4.66 Time building geometry restraints manager: 10.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2127 1.29 - 1.42: 3396 1.42 - 1.55: 7280 1.55 - 1.68: 17 1.68 - 1.81: 108 Bond restraints: 12928 Sorted by residual: bond pdb=" C ALA B 110 " pdb=" N PRO B 111 " ideal model delta sigma weight residual 1.333 1.409 -0.076 1.17e-02 7.31e+03 4.25e+01 bond pdb=" C ALA D 110 " pdb=" N PRO D 111 " ideal model delta sigma weight residual 1.333 1.408 -0.076 1.17e-02 7.31e+03 4.20e+01 bond pdb=" C ALA A 110 " pdb=" N PRO A 111 " ideal model delta sigma weight residual 1.333 1.408 -0.076 1.17e-02 7.31e+03 4.18e+01 bond pdb=" C ALA C 110 " pdb=" N PRO C 111 " ideal model delta sigma weight residual 1.333 1.408 -0.076 1.17e-02 7.31e+03 4.17e+01 bond pdb=" C PHE C 361 " pdb=" N PRO C 362 " ideal model delta sigma weight residual 1.335 1.406 -0.071 1.15e-02 7.56e+03 3.82e+01 ... (remaining 12923 not shown) Histogram of bond angle deviations from ideal: 96.81 - 105.83: 478 105.83 - 114.84: 7265 114.84 - 123.86: 9425 123.86 - 132.88: 376 132.88 - 141.89: 56 Bond angle restraints: 17600 Sorted by residual: angle pdb=" C PHE D 361 " pdb=" N PRO D 362 " pdb=" CA PRO D 362 " ideal model delta sigma weight residual 119.66 113.23 6.43 7.20e-01 1.93e+00 7.98e+01 angle pdb=" C PHE A 361 " pdb=" N PRO A 362 " pdb=" CA PRO A 362 " ideal model delta sigma weight residual 119.66 113.23 6.43 7.20e-01 1.93e+00 7.98e+01 angle pdb=" C PHE B 361 " pdb=" N PRO B 362 " pdb=" CA PRO B 362 " ideal model delta sigma weight residual 119.66 113.23 6.43 7.20e-01 1.93e+00 7.97e+01 angle pdb=" C PHE C 361 " pdb=" N PRO C 362 " pdb=" CA PRO C 362 " ideal model delta sigma weight residual 119.66 113.29 6.37 7.20e-01 1.93e+00 7.82e+01 angle pdb=" N SER D 339 " pdb=" CA SER D 339 " pdb=" C SER D 339 " ideal model delta sigma weight residual 111.36 120.50 -9.14 1.09e+00 8.42e-01 7.03e+01 ... (remaining 17595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6626 17.94 - 35.87: 778 35.87 - 53.81: 264 53.81 - 71.75: 56 71.75 - 89.68: 28 Dihedral angle restraints: 7752 sinusoidal: 3100 harmonic: 4652 Sorted by residual: dihedral pdb=" CH3 ACE C 0 " pdb=" C ACE C 0 " pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sinusoidal sigma weight residual 180.00 -160.61 -19.39 1 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CH3 ACE D 0 " pdb=" C ACE D 0 " pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sinusoidal sigma weight residual -180.00 -160.66 -19.34 1 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CH3 ACE A 0 " pdb=" C ACE A 0 " pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sinusoidal sigma weight residual -180.00 -160.68 -19.32 1 5.00e+00 4.00e-02 2.16e+01 ... (remaining 7749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1286 0.089 - 0.179: 466 0.179 - 0.268: 151 0.268 - 0.357: 49 0.357 - 0.447: 36 Chirality restraints: 1988 Sorted by residual: chirality pdb=" CA LYS C 17 " pdb=" N LYS C 17 " pdb=" C LYS C 17 " pdb=" CB LYS C 17 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.99e+00 chirality pdb=" CA LYS D 17 " pdb=" N LYS D 17 " pdb=" C LYS D 17 " pdb=" CB LYS D 17 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" CA LYS A 17 " pdb=" N LYS A 17 " pdb=" C LYS A 17 " pdb=" CB LYS A 17 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.93e+00 ... (remaining 1985 not shown) Planarity restraints: 2320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ACE C 0 " -0.031 2.00e-02 2.50e+03 1.01e-01 1.28e+02 pdb=" O ACE C 0 " -0.024 2.00e-02 2.50e+03 pdb=" CH3 ACE C 0 " 0.092 2.00e-02 2.50e+03 pdb=" N MET C 1 " -0.161 2.00e-02 2.50e+03 pdb=" CA MET C 1 " 0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE D 0 " -0.030 2.00e-02 2.50e+03 1.01e-01 1.28e+02 pdb=" O ACE D 0 " -0.024 2.00e-02 2.50e+03 pdb=" CH3 ACE D 0 " 0.091 2.00e-02 2.50e+03 pdb=" N MET D 1 " -0.161 2.00e-02 2.50e+03 pdb=" CA MET D 1 " 0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE A 0 " -0.030 2.00e-02 2.50e+03 1.01e-01 1.28e+02 pdb=" O ACE A 0 " -0.024 2.00e-02 2.50e+03 pdb=" CH3 ACE A 0 " 0.091 2.00e-02 2.50e+03 pdb=" N MET A 1 " -0.161 2.00e-02 2.50e+03 pdb=" CA MET A 1 " 0.124 2.00e-02 2.50e+03 ... (remaining 2317 not shown) Histogram of nonbonded interaction distances: 0.10 - 1.06: 684 1.06 - 2.02: 3944 2.02 - 2.98: 17670 2.98 - 3.94: 54732 3.94 - 4.90: 103749 Warning: very small nonbonded interaction distances. Nonbonded interactions: 180779 Sorted by model distance: nonbonded pdb=" CG GLN B 351 " pdb=" C MET A 365 " model vdw 0.104 3.670 nonbonded pdb=" CB LEU B 7 " pdb=" C LEU C 254 " model vdw 0.139 3.670 nonbonded pdb=" O ASP B 337 " pdb=" C GLU C 327 " model vdw 0.141 3.270 nonbonded pdb=" CB PHE B 152 " pdb=" O PRO C 155 " model vdw 0.209 3.440 nonbonded pdb="CA CA A 503 " pdb="CA CA D 503 " model vdw 0.216 1.980 ... (remaining 180774 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 8 9.91 5 Zn 4 6.06 5 S 60 5.16 5 Cl 4 4.86 5 C 8016 2.51 5 N 2184 2.21 5 O 2808 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.070 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: 0.020 Extract box with map and model: 1.600 Check model and map are aligned: 0.180 Convert atoms to be neutral: 0.100 Process input model: 47.010 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:10.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 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 : 0.020 0.084 12928 Z= 1.328 Angle : 1.797 17.372 17600 Z= 1.165 Chirality : 0.120 0.447 1988 Planarity : 0.009 0.101 2320 Dihedral : 18.551 89.683 4728 Min Nonbonded Distance : 0.104 Molprobity Statistics. All-atom Clashscore : 287.40 Ramachandran Plot: Outliers : 0.76 % Allowed : 1.27 % Favored : 97.97 % Rotamer Outliers : 6.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.95 (0.21), residues: 1580 helix: 2.81 (0.20), residues: 516 sheet: 1.84 (0.26), residues: 424 loop : -0.41 (0.23), residues: 640 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 284 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 48 residues processed: 344 average time/residue: 1.3163 time to fit residues: 493.1755 Evaluate side-chains 232 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 184 time to evaluate : 1.607 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 45 residues processed: 13 average time/residue: 1.1173 time to fit residues: 17.9471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 5.9990 chunk 151 optimal weight: 20.0000 chunk 84 optimal weight: 40.0000 chunk 51 optimal weight: 50.0000 chunk 102 optimal weight: 7.9990 chunk 80 optimal weight: 0.0670 chunk 156 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 50.0000 chunk 116 optimal weight: 8.9990 chunk 181 optimal weight: 50.0000 overall best weight: 3.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN A 146 GLN A 167 ASN ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN C 175 ASN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 GLN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN ** D 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5333 moved from start: 0.9948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.050 1.362 12928 Z= 3.256 Angle : 4.209 63.012 17600 Z= 2.395 Chirality : 0.241 2.551 1988 Planarity : 0.032 0.362 2320 Dihedral : 16.610 146.327 1736 Min Nonbonded Distance : 1.151 Molprobity Statistics. All-atom Clashscore : 353.19 Ramachandran Plot: Outliers : 8.61 % Allowed : 14.68 % Favored : 76.71 % Rotamer Outliers : 21.07 % Cbeta Deviations : 8.33 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 11.25 % Twisted General : 7.45 % 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: -5.10 (0.17), residues: 1580 helix: -3.63 (0.17), residues: 378 sheet: -1.62 (0.31), residues: 260 loop : -4.03 (0.16), residues: 942 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 312 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 295 outliers final: 105 residues processed: 532 average time/residue: 0.9253 time to fit residues: 553.5772 Evaluate side-chains 358 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 253 time to evaluate : 1.454 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 96 residues processed: 13 average time/residue: 0.3370 time to fit residues: 7.8954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 chunk 196 optimal weight: 50.0000 chunk 162 optimal weight: 3.9990 chunk 180 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 145 optimal weight: 50.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 ASN ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN D 175 ASN D 206 GLN ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5085 moved from start: 1.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.038 1.206 12928 Z= 2.517 Angle : 3.290 54.939 17600 Z= 1.908 Chirality : 0.204 4.256 1988 Planarity : 0.022 0.271 2320 Dihedral : 16.019 178.528 1736 Min Nonbonded Distance : 1.110 Molprobity Statistics. All-atom Clashscore : 258.39 Ramachandran Plot: Outliers : 3.92 % Allowed : 16.33 % Favored : 79.75 % Rotamer Outliers : 19.36 % Cbeta Deviations : 5.29 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 7.50 % Twisted General : 7.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.47 (0.18), residues: 1580 helix: -2.58 (0.21), residues: 414 sheet: -1.15 (0.30), residues: 295 loop : -4.03 (0.17), residues: 871 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 288 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 271 outliers final: 111 residues processed: 492 average time/residue: 0.9758 time to fit residues: 537.3066 Evaluate side-chains 360 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 249 time to evaluate : 1.583 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 111 outliers final: 88 residues processed: 24 average time/residue: 0.4833 time to fit residues: 16.3707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 8.9990 chunk 136 optimal weight: 0.3980 chunk 94 optimal weight: 50.0000 chunk 20 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 122 optimal weight: 30.0000 chunk 182 optimal weight: 6.9990 chunk 193 optimal weight: 50.0000 chunk 95 optimal weight: 50.0000 chunk 173 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 overall best weight: 5.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4937 moved from start: 1.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.035 1.196 12928 Z= 2.316 Angle : 2.957 53.317 17600 Z= 1.722 Chirality : 0.173 3.583 1988 Planarity : 0.018 0.234 2320 Dihedral : 15.571 171.658 1736 Min Nonbonded Distance : 1.147 Molprobity Statistics. All-atom Clashscore : 223.60 Ramachandran Plot: Outliers : 3.10 % Allowed : 17.09 % Favored : 79.81 % Rotamer Outliers : 18.93 % Cbeta Deviations : 3.64 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 7.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.19), residues: 1580 helix: -1.87 (0.24), residues: 408 sheet: -0.89 (0.31), residues: 277 loop : -3.84 (0.18), residues: 895 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 269 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 265 outliers final: 117 residues processed: 480 average time/residue: 0.9708 time to fit residues: 521.9641 Evaluate side-chains 348 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 231 time to evaluate : 1.476 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 117 outliers final: 99 residues processed: 20 average time/residue: 0.5129 time to fit residues: 14.5434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 30.0000 chunk 109 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 143 optimal weight: 50.0000 chunk 79 optimal weight: 9.9990 chunk 164 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 50.0000 chunk 173 optimal weight: 5.9990 chunk 48 optimal weight: 50.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 ASN ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4907 moved from start: 1.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.034 1.180 12928 Z= 2.224 Angle : 2.748 49.093 17600 Z= 1.627 Chirality : 0.175 3.922 1988 Planarity : 0.017 0.246 2320 Dihedral : 15.311 172.158 1736 Min Nonbonded Distance : 1.107 Molprobity Statistics. All-atom Clashscore : 206.90 Ramachandran Plot: Outliers : 2.41 % Allowed : 17.72 % Favored : 79.87 % Rotamer Outliers : 16.57 % Cbeta Deviations : 3.51 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 6.78 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.19), residues: 1580 helix: -1.41 (0.25), residues: 411 sheet: -0.76 (0.32), residues: 252 loop : -3.84 (0.18), residues: 917 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 245 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 232 outliers final: 114 residues processed: 425 average time/residue: 1.0195 time to fit residues: 485.5483 Evaluate side-chains 329 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 215 time to evaluate : 1.604 Switching outliers to nearest non-outliers outliers start: 114 outliers final: 93 residues processed: 21 average time/residue: 0.7275 time to fit residues: 20.0167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 10.0000 chunk 174 optimal weight: 20.0000 chunk 38 optimal weight: 30.0000 chunk 113 optimal weight: 30.0000 chunk 47 optimal weight: 50.0000 chunk 193 optimal weight: 50.0000 chunk 160 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN ** C 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4878 moved from start: 1.5970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.033 1.178 12928 Z= 2.157 Angle : 2.663 50.856 17600 Z= 1.572 Chirality : 0.166 3.046 1988 Planarity : 0.017 0.214 2320 Dihedral : 15.119 171.668 1736 Min Nonbonded Distance : 1.059 Molprobity Statistics. All-atom Clashscore : 192.78 Ramachandran Plot: Outliers : 2.22 % Allowed : 18.86 % Favored : 78.92 % Rotamer Outliers : 14.93 % Cbeta Deviations : 2.84 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 6.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.19), residues: 1580 helix: -1.35 (0.25), residues: 414 sheet: -0.52 (0.33), residues: 247 loop : -3.94 (0.17), residues: 919 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 231 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 209 outliers final: 109 residues processed: 399 average time/residue: 0.9785 time to fit residues: 437.0226 Evaluate side-chains 335 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 226 time to evaluate : 1.541 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 109 outliers final: 91 residues processed: 20 average time/residue: 0.5218 time to fit residues: 14.7961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 141 optimal weight: 50.0000 chunk 109 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 192 optimal weight: 50.0000 chunk 120 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 ASN ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4780 moved from start: 1.6726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.033 1.171 12928 Z= 2.139 Angle : 2.580 43.716 17600 Z= 1.527 Chirality : 0.177 3.710 1988 Planarity : 0.016 0.210 2320 Dihedral : 14.869 172.886 1736 Min Nonbonded Distance : 1.120 Molprobity Statistics. All-atom Clashscore : 182.94 Ramachandran Plot: Outliers : 2.03 % Allowed : 18.86 % Favored : 79.11 % Rotamer Outliers : 12.93 % Cbeta Deviations : 2.84 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 6.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.20), residues: 1580 helix: -1.27 (0.25), residues: 407 sheet: -0.27 (0.36), residues: 214 loop : -3.79 (0.18), residues: 959 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 252 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 181 outliers final: 102 residues processed: 398 average time/residue: 0.9748 time to fit residues: 435.0646 Evaluate side-chains 315 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 213 time to evaluate : 1.532 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 85 residues processed: 17 average time/residue: 0.5893 time to fit residues: 14.0051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 131 optimal weight: 50.0000 chunk 95 optimal weight: 50.0000 chunk 17 optimal weight: 8.9990 chunk 151 optimal weight: 20.0000 chunk 175 optimal weight: 0.4980 overall best weight: 6.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 GLN A 213 GLN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN D 44 ASN D 206 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4792 moved from start: 1.7408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.032 1.175 12928 Z= 2.124 Angle : 2.542 44.142 17600 Z= 1.501 Chirality : 0.164 2.519 1988 Planarity : 0.016 0.205 2320 Dihedral : 14.854 170.548 1736 Min Nonbonded Distance : 1.071 Molprobity Statistics. All-atom Clashscore : 180.34 Ramachandran Plot: Outliers : 1.96 % Allowed : 18.10 % Favored : 79.94 % Rotamer Outliers : 12.14 % Cbeta Deviations : 2.71 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 8.75 % Twisted General : 5.92 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.20), residues: 1580 helix: -1.26 (0.25), residues: 413 sheet: -0.68 (0.34), residues: 229 loop : -3.68 (0.18), residues: 938 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 232 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 170 outliers final: 100 residues processed: 363 average time/residue: 1.0255 time to fit residues: 418.2834 Evaluate side-chains 321 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 221 time to evaluate : 1.648 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 83 residues processed: 19 average time/residue: 0.6632 time to fit residues: 17.1443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 6.9990 chunk 168 optimal weight: 30.0000 chunk 179 optimal weight: 20.0000 chunk 108 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 141 optimal weight: 50.0000 chunk 55 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 chunk 169 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 chunk 189 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 GLN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4753 moved from start: 1.7846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.032 1.169 12928 Z= 2.114 Angle : 2.551 42.128 17600 Z= 1.494 Chirality : 0.159 3.640 1988 Planarity : 0.016 0.204 2320 Dihedral : 14.813 171.398 1736 Min Nonbonded Distance : 1.112 Molprobity Statistics. All-atom Clashscore : 174.83 Ramachandran Plot: Outliers : 1.52 % Allowed : 18.92 % Favored : 79.56 % Rotamer Outliers : 9.07 % Cbeta Deviations : 2.78 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 6.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.20), residues: 1580 helix: -1.11 (0.26), residues: 393 sheet: -0.89 (0.33), residues: 253 loop : -3.62 (0.19), residues: 934 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 223 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 127 outliers final: 90 residues processed: 326 average time/residue: 1.0822 time to fit residues: 392.9943 Evaluate side-chains 306 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 216 time to evaluate : 1.532 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 76 residues processed: 16 average time/residue: 0.6720 time to fit residues: 14.8822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 20.0000 chunk 90 optimal weight: 50.0000 chunk 132 optimal weight: 30.0000 chunk 199 optimal weight: 50.0000 chunk 183 optimal weight: 8.9990 chunk 158 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 97 optimal weight: 50.0000 chunk 126 optimal weight: 9.9990 chunk 169 optimal weight: 20.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4793 moved from start: 1.8117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.032 1.172 12928 Z= 2.124 Angle : 2.553 41.057 17600 Z= 1.496 Chirality : 0.162 3.427 1988 Planarity : 0.016 0.205 2320 Dihedral : 14.923 171.329 1736 Min Nonbonded Distance : 1.075 Molprobity Statistics. All-atom Clashscore : 174.11 Ramachandran Plot: Outliers : 1.39 % Allowed : 18.73 % Favored : 79.87 % Rotamer Outliers : 7.71 % Cbeta Deviations : 2.58 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 5.92 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.20), residues: 1580 helix: -1.48 (0.25), residues: 419 sheet: -0.87 (0.34), residues: 240 loop : -3.62 (0.18), residues: 921 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 232 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 87 residues processed: 319 average time/residue: 1.0954 time to fit residues: 387.7806 Evaluate side-chains 300 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 213 time to evaluate : 1.563 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 75 residues processed: 13 average time/residue: 0.6278 time to fit residues: 11.8177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 50.0000 chunk 146 optimal weight: 50.0000 chunk 23 optimal weight: 20.0000 chunk 44 optimal weight: 50.0000 chunk 158 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 29 optimal weight: 40.0000 chunk 139 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.231216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.184903 restraints weight = 24030.698| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 5.09 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 1.8320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.032 1.176 12928 Z= 2.122 Angle : 2.576 46.219 17600 Z= 1.494 Chirality : 0.170 4.269 1988 Planarity : 0.015 0.202 2320 Dihedral : 15.027 171.493 1736 Min Nonbonded Distance : 1.083 Molprobity Statistics. All-atom Clashscore : 172.48 Ramachandran Plot: Outliers : 1.52 % Allowed : 19.43 % Favored : 79.05 % Rotamer Outliers : 7.57 % Cbeta Deviations : 2.71 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 6.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.20), residues: 1580 helix: -1.42 (0.25), residues: 418 sheet: -0.98 (0.34), residues: 236 loop : -3.65 (0.18), residues: 926 =============================================================================== Job complete usr+sys time: 6559.88 seconds wall clock time: 118 minutes 7.00 seconds (7087.00 seconds total)