Starting phenix.real_space_refine on Thu Mar 14 15:20:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6r_36012/03_2024/8j6r_36012_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6r_36012/03_2024/8j6r_36012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6r_36012/03_2024/8j6r_36012.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6r_36012/03_2024/8j6r_36012.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6r_36012/03_2024/8j6r_36012_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6r_36012/03_2024/8j6r_36012_updated.pdb" } resolution = 2.76 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= 0.002 sd= 0.034 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 69 5.16 5 C 5811 2.51 5 N 1554 2.21 5 O 1686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 9120 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1795 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Chain: "R" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2420 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 284} Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'FI7': 1, 'NAG': 1} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.09, per 1000 atoms: 0.56 Number of scatterers: 9120 At special positions: 0 Unit cell: (108.498, 122.694, 112.554, 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 69 16.00 O 1686 8.00 N 1554 7.00 C 5811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.04 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " 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 Links applied NAG-ASN " NAG R 402 " - " ASN R 17 " Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.6 seconds 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 13 sheets defined 33.4% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 4.297A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 removed outlier: 3.805A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.003A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'B' and resid 4 through 24 removed outlier: 4.512A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing helix chain 'R' and resid 24 through 54 Proline residue: R 31 - end of helix Processing helix chain 'R' and resid 61 through 89 removed outlier: 4.304A pdb=" N CYS R 79 " --> pdb=" O LEU R 75 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU R 80 " --> pdb=" O LEU R 76 " (cutoff:3.500A) Proline residue: R 81 - end of helix removed outlier: 3.825A pdb=" N ARG R 89 " --> pdb=" O ASP R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 129 Processing helix chain 'R' and resid 135 through 138 Processing helix chain 'R' and resid 141 through 162 removed outlier: 5.183A pdb=" N HIS R 161 " --> pdb=" O GLY R 157 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU R 162 " --> pdb=" O LEU R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 217 removed outlier: 3.798A pdb=" N LEU R 194 " --> pdb=" O GLU R 190 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Proline residue: R 200 - end of helix Processing helix chain 'R' and resid 220 through 222 No H-bonds generated for 'chain 'R' and resid 220 through 222' Processing helix chain 'R' and resid 224 through 260 Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 266 through 268 No H-bonds generated for 'chain 'R' and resid 266 through 268' Processing helix chain 'R' and resid 270 through 294 removed outlier: 3.812A pdb=" N PHE R 277 " --> pdb=" O ASP R 273 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER R 287 " --> pdb=" O THR R 283 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.760A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.970A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.017A 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: 7.104A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.147A 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: 6.649A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.084A 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: 6.850A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.400A 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: 6.667A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.470A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.569A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.213A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.498A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'S' and resid 155 through 160 removed outlier: 3.786A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 225 through 231 removed outlier: 3.693A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1137 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: 2.60 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2928 1.34 - 1.46: 2278 1.46 - 1.58: 4012 1.58 - 1.71: 1 1.71 - 1.83: 100 Bond restraints: 9319 Sorted by residual: bond pdb=" C20 FI7 R 401 " pdb=" N19 FI7 R 401 " ideal model delta sigma weight residual 1.396 1.486 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C07 FI7 R 401 " pdb=" C08 FI7 R 401 " ideal model delta sigma weight residual 1.466 1.546 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C04 FI7 R 401 " pdb=" C05 FI7 R 401 " ideal model delta sigma weight residual 1.483 1.563 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C05 FI7 R 401 " pdb=" O16 FI7 R 401 " ideal model delta sigma weight residual 1.330 1.406 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C17 FI7 R 401 " pdb=" N19 FI7 R 401 " ideal model delta sigma weight residual 1.348 1.420 -0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 9314 not shown) Histogram of bond angle deviations from ideal: 99.53 - 107.00: 207 107.00 - 114.46: 5464 114.46 - 121.93: 4923 121.93 - 129.40: 1939 129.40 - 136.86: 77 Bond angle restraints: 12610 Sorted by residual: angle pdb=" C MET R 167 " pdb=" N PRO R 168 " pdb=" CA PRO R 168 " ideal model delta sigma weight residual 127.00 136.86 -9.86 2.40e+00 1.74e-01 1.69e+01 angle pdb=" C ASP R 14 " pdb=" N LYS R 15 " pdb=" CA LYS R 15 " ideal model delta sigma weight residual 121.54 129.12 -7.58 1.91e+00 2.74e-01 1.57e+01 angle pdb=" C MET R 167 " pdb=" N PRO R 168 " pdb=" CD PRO R 168 " ideal model delta sigma weight residual 120.60 112.67 7.93 2.20e+00 2.07e-01 1.30e+01 angle pdb=" C02 FI7 R 401 " pdb=" C17 FI7 R 401 " pdb=" N19 FI7 R 401 " ideal model delta sigma weight residual 113.44 123.58 -10.14 3.00e+00 1.11e-01 1.14e+01 angle pdb=" N HIS R 184 " pdb=" CA HIS R 184 " pdb=" C HIS R 184 " ideal model delta sigma weight residual 111.30 115.76 -4.46 1.36e+00 5.41e-01 1.08e+01 ... (remaining 12605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 4976 16.57 - 33.13: 451 33.13 - 49.70: 102 49.70 - 66.26: 17 66.26 - 82.83: 7 Dihedral angle restraints: 5553 sinusoidal: 2218 harmonic: 3335 Sorted by residual: dihedral pdb=" CB CYS R 100 " pdb=" SG CYS R 100 " pdb=" SG CYS R 177 " pdb=" CB CYS R 177 " ideal model delta sinusoidal sigma weight residual 93.00 138.69 -45.69 1 1.00e+01 1.00e-02 2.89e+01 dihedral pdb=" CB CYS R 18 " pdb=" SG CYS R 18 " pdb=" SG CYS R 183 " pdb=" CB CYS R 183 " ideal model delta sinusoidal sigma weight residual 93.00 53.83 39.17 1 1.00e+01 1.00e-02 2.16e+01 dihedral pdb=" CA PHE A 323 " pdb=" C PHE A 323 " pdb=" N THR A 324 " pdb=" CA THR A 324 " ideal model delta harmonic sigma weight residual -180.00 -160.03 -19.97 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 5550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.244: 1411 0.244 - 0.489: 0 0.489 - 0.733: 0 0.733 - 0.977: 0 0.977 - 1.222: 1 Chirality restraints: 1412 Sorted by residual: chirality pdb=" C1 NAG R 402 " pdb=" ND2 ASN R 17 " pdb=" C2 NAG R 402 " pdb=" O5 NAG R 402 " both_signs ideal model delta sigma weight residual False -2.40 -1.18 -1.22 2.00e-01 2.50e+01 3.73e+01 chirality pdb=" CA TRP R 59 " pdb=" N TRP R 59 " pdb=" C TRP R 59 " pdb=" CB TRP R 59 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA TYR S 190 " pdb=" N TYR S 190 " pdb=" C TYR S 190 " pdb=" CB TYR S 190 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1409 not shown) Planarity restraints: 1595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 402 " 0.350 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG R 402 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG R 402 " 0.154 2.00e-02 2.50e+03 pdb=" N2 NAG R 402 " -0.533 2.00e-02 2.50e+03 pdb=" O7 NAG R 402 " 0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.059 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO S 75 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 17 " 0.026 2.00e-02 2.50e+03 2.89e-02 1.05e+01 pdb=" CG ASN R 17 " -0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN R 17 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN R 17 " -0.047 2.00e-02 2.50e+03 pdb=" C1 NAG R 402 " 0.035 2.00e-02 2.50e+03 ... (remaining 1592 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 137 2.67 - 3.23: 8098 3.23 - 3.79: 13952 3.79 - 4.34: 18785 4.34 - 4.90: 32054 Nonbonded interactions: 73026 Sorted by model distance: nonbonded pdb=" O GLU R 196 " pdb=" CG PRO R 200 " model vdw 2.116 3.440 nonbonded pdb=" O GLU R 196 " pdb=" CD PRO R 200 " model vdw 2.125 3.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.208 2.440 nonbonded pdb=" O LYS R 60 " pdb=" N ARG R 63 " model vdw 2.228 2.520 nonbonded pdb=" O LEU B 30 " pdb=" OG1 THR B 34 " model vdw 2.280 2.440 ... (remaining 73021 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: 0.290 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: 0.010 Extract box with map and model: 1.960 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.540 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 9319 Z= 0.282 Angle : 0.625 10.140 12610 Z= 0.325 Chirality : 0.055 1.222 1412 Planarity : 0.009 0.300 1594 Dihedral : 13.554 82.831 3382 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.52 (0.25), residues: 1137 helix: 1.31 (0.27), residues: 387 sheet: 0.50 (0.31), residues: 295 loop : -0.53 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 59 HIS 0.004 0.001 HIS R 161 PHE 0.015 0.001 PHE R 52 TYR 0.016 0.001 TYR S 190 ARG 0.004 0.000 ARG R 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.038 Fit side-chains REVERT: A 25 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6707 (mm-30) REVERT: A 28 GLU cc_start: 0.6756 (mp0) cc_final: 0.6365 (mp0) REVERT: A 270 LYS cc_start: 0.8072 (mtmm) cc_final: 0.7775 (mttm) REVERT: A 337 ASP cc_start: 0.7542 (m-30) cc_final: 0.7334 (m-30) REVERT: B 89 LYS cc_start: 0.8421 (mttp) cc_final: 0.8198 (mttt) REVERT: B 254 ASP cc_start: 0.7008 (t70) cc_final: 0.6596 (t0) REVERT: B 268 ASN cc_start: 0.7227 (m110) cc_final: 0.7021 (m110) REVERT: S 219 LEU cc_start: 0.8014 (tt) cc_final: 0.7812 (tt) REVERT: R 22 ARG cc_start: 0.6712 (mtm-85) cc_final: 0.6482 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 1.1248 time to fit residues: 246.4633 Evaluate side-chains 190 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 0.0570 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 65 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN B 176 GLN S 82 GLN S 186 GLN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 9319 Z= 0.155 Angle : 0.489 6.486 12610 Z= 0.260 Chirality : 0.041 0.173 1412 Planarity : 0.004 0.069 1594 Dihedral : 5.042 40.038 1290 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.61 % Allowed : 9.85 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.75 (0.25), residues: 1137 helix: 1.63 (0.27), residues: 387 sheet: 0.65 (0.31), residues: 284 loop : -0.51 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 59 HIS 0.005 0.001 HIS R 161 PHE 0.009 0.001 PHE B 199 TYR 0.022 0.001 TYR S 190 ARG 0.008 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 193 time to evaluate : 0.862 Fit side-chains REVERT: A 190 THR cc_start: 0.8427 (t) cc_final: 0.8202 (m) REVERT: A 270 LYS cc_start: 0.8065 (mtmm) cc_final: 0.7778 (mtmm) REVERT: A 337 ASP cc_start: 0.7563 (m-30) cc_final: 0.7325 (m-30) REVERT: B 254 ASP cc_start: 0.6935 (t70) cc_final: 0.6597 (t0) REVERT: B 268 ASN cc_start: 0.7251 (m110) cc_final: 0.7034 (m110) REVERT: S 140 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7367 (mtm) REVERT: R 146 ILE cc_start: 0.6824 (OUTLIER) cc_final: 0.6443 (mp) outliers start: 16 outliers final: 6 residues processed: 199 average time/residue: 1.2084 time to fit residues: 255.8542 Evaluate side-chains 198 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 190 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 192 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.0980 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN B 340 ASN S 82 GLN R 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9319 Z= 0.151 Angle : 0.469 6.225 12610 Z= 0.251 Chirality : 0.041 0.169 1412 Planarity : 0.004 0.063 1594 Dihedral : 4.906 43.714 1290 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.01 % Allowed : 11.96 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.80 (0.25), residues: 1137 helix: 1.69 (0.27), residues: 389 sheet: 0.65 (0.31), residues: 284 loop : -0.50 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 PHE 0.008 0.001 PHE R 117 TYR 0.021 0.001 TYR S 190 ARG 0.008 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 193 time to evaluate : 0.928 Fit side-chains REVERT: A 270 LYS cc_start: 0.8100 (mtmm) cc_final: 0.7803 (mtmm) REVERT: A 337 ASP cc_start: 0.7621 (m-30) cc_final: 0.7370 (m-30) REVERT: B 158 VAL cc_start: 0.8643 (p) cc_final: 0.8293 (t) REVERT: B 254 ASP cc_start: 0.6909 (t70) cc_final: 0.6588 (t0) REVERT: B 268 ASN cc_start: 0.7270 (m110) cc_final: 0.7052 (m110) REVERT: S 140 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7397 (mtm) REVERT: R 146 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6440 (mp) outliers start: 20 outliers final: 10 residues processed: 201 average time/residue: 1.2623 time to fit residues: 270.0726 Evaluate side-chains 205 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 193 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 146 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 0.0870 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 96 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9319 Z= 0.309 Angle : 0.554 8.205 12610 Z= 0.293 Chirality : 0.044 0.228 1412 Planarity : 0.004 0.065 1594 Dihedral : 5.302 48.779 1290 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.71 % Allowed : 13.87 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.55 (0.25), residues: 1137 helix: 1.43 (0.27), residues: 389 sheet: 0.60 (0.30), residues: 292 loop : -0.69 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.006 0.001 HIS A 188 PHE 0.018 0.002 PHE R 117 TYR 0.025 0.002 TYR B 105 ARG 0.007 0.001 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 196 time to evaluate : 0.905 Fit side-chains REVERT: A 270 LYS cc_start: 0.8078 (mtmm) cc_final: 0.7790 (mtmm) REVERT: A 337 ASP cc_start: 0.7598 (m-30) cc_final: 0.7344 (m-30) REVERT: B 254 ASP cc_start: 0.6993 (t70) cc_final: 0.6640 (t0) REVERT: S 140 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7434 (mtm) REVERT: R 146 ILE cc_start: 0.6831 (OUTLIER) cc_final: 0.6453 (mp) outliers start: 17 outliers final: 11 residues processed: 205 average time/residue: 1.2165 time to fit residues: 265.4335 Evaluate side-chains 204 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 233 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9319 Z= 0.248 Angle : 0.524 7.038 12610 Z= 0.280 Chirality : 0.043 0.209 1412 Planarity : 0.004 0.063 1594 Dihedral : 5.300 49.151 1290 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.51 % Allowed : 15.58 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1137 helix: 1.44 (0.27), residues: 389 sheet: 0.56 (0.30), residues: 292 loop : -0.68 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.005 0.001 HIS A 188 PHE 0.012 0.001 PHE R 117 TYR 0.024 0.002 TYR S 190 ARG 0.009 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 194 time to evaluate : 1.124 Fit side-chains REVERT: A 270 LYS cc_start: 0.8091 (mtmm) cc_final: 0.7827 (mttm) REVERT: A 337 ASP cc_start: 0.7647 (m-30) cc_final: 0.7381 (m-30) REVERT: B 254 ASP cc_start: 0.6979 (t70) cc_final: 0.6614 (t70) REVERT: S 140 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7409 (mtm) REVERT: R 146 ILE cc_start: 0.6804 (OUTLIER) cc_final: 0.6428 (mp) outliers start: 25 outliers final: 11 residues processed: 208 average time/residue: 1.2691 time to fit residues: 280.2705 Evaluate side-chains 207 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 194 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 233 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9319 Z= 0.186 Angle : 0.496 6.260 12610 Z= 0.266 Chirality : 0.042 0.186 1412 Planarity : 0.004 0.061 1594 Dihedral : 5.186 48.632 1290 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.21 % Allowed : 16.78 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.64 (0.25), residues: 1137 helix: 1.52 (0.27), residues: 389 sheet: 0.60 (0.30), residues: 292 loop : -0.62 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 188 HIS 0.004 0.001 HIS A 188 PHE 0.009 0.001 PHE R 276 TYR 0.022 0.001 TYR S 190 ARG 0.011 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 190 time to evaluate : 0.920 Fit side-chains REVERT: A 270 LYS cc_start: 0.8085 (mtmm) cc_final: 0.7836 (mttm) REVERT: A 337 ASP cc_start: 0.7641 (m-30) cc_final: 0.7377 (m-30) REVERT: B 254 ASP cc_start: 0.6917 (t70) cc_final: 0.6595 (t70) REVERT: B 285 LEU cc_start: 0.8593 (tp) cc_final: 0.8380 (tt) REVERT: S 38 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7729 (ptt180) REVERT: S 140 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7403 (mtm) REVERT: R 146 ILE cc_start: 0.6797 (OUTLIER) cc_final: 0.6418 (mp) outliers start: 22 outliers final: 12 residues processed: 202 average time/residue: 1.2160 time to fit residues: 261.5099 Evaluate side-chains 205 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 190 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 233 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 91 optimal weight: 0.0570 chunk 60 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9319 Z= 0.164 Angle : 0.487 6.781 12610 Z= 0.262 Chirality : 0.041 0.177 1412 Planarity : 0.004 0.060 1594 Dihedral : 5.068 48.105 1290 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.51 % Allowed : 17.29 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 (0.25), residues: 1137 helix: 1.64 (0.27), residues: 388 sheet: 0.59 (0.30), residues: 296 loop : -0.56 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 188 HIS 0.003 0.001 HIS A 188 PHE 0.008 0.001 PHE R 276 TYR 0.021 0.001 TYR S 190 ARG 0.012 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 188 time to evaluate : 0.941 Fit side-chains REVERT: A 270 LYS cc_start: 0.8059 (mtmm) cc_final: 0.7790 (mttm) REVERT: A 337 ASP cc_start: 0.7630 (m-30) cc_final: 0.7382 (m-30) REVERT: B 254 ASP cc_start: 0.6890 (t70) cc_final: 0.6584 (t70) REVERT: B 285 LEU cc_start: 0.8582 (tp) cc_final: 0.8375 (tt) REVERT: S 38 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7690 (ptt180) REVERT: S 140 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7407 (mtm) REVERT: R 146 ILE cc_start: 0.6794 (OUTLIER) cc_final: 0.6419 (mp) outliers start: 25 outliers final: 13 residues processed: 201 average time/residue: 1.2249 time to fit residues: 262.2110 Evaluate side-chains 202 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 186 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 233 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN S 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9319 Z= 0.326 Angle : 0.566 7.570 12610 Z= 0.302 Chirality : 0.044 0.221 1412 Planarity : 0.004 0.061 1594 Dihedral : 5.428 52.647 1290 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.31 % Allowed : 17.49 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.49 (0.25), residues: 1137 helix: 1.40 (0.27), residues: 388 sheet: 0.51 (0.29), residues: 297 loop : -0.69 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS A 188 PHE 0.017 0.002 PHE R 117 TYR 0.023 0.002 TYR S 190 ARG 0.007 0.001 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 196 time to evaluate : 0.970 Fit side-chains REVERT: A 270 LYS cc_start: 0.8038 (mtmm) cc_final: 0.7770 (mttm) REVERT: A 337 ASP cc_start: 0.7666 (m-30) cc_final: 0.7413 (m-30) REVERT: B 254 ASP cc_start: 0.6988 (t70) cc_final: 0.6633 (t70) REVERT: S 38 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7758 (ptt180) REVERT: S 140 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7553 (mtm) REVERT: R 146 ILE cc_start: 0.6795 (OUTLIER) cc_final: 0.6423 (mp) outliers start: 23 outliers final: 16 residues processed: 208 average time/residue: 1.3014 time to fit residues: 287.4772 Evaluate side-chains 216 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 197 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 233 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 60 optimal weight: 0.0970 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.0000 chunk 30 optimal weight: 0.2980 chunk 90 optimal weight: 4.9990 chunk 95 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 overall best weight: 0.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9319 Z= 0.134 Angle : 0.482 9.117 12610 Z= 0.263 Chirality : 0.041 0.173 1412 Planarity : 0.004 0.060 1594 Dihedral : 4.910 46.107 1290 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.91 % Allowed : 18.39 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.79 (0.25), residues: 1137 helix: 1.68 (0.27), residues: 389 sheet: 0.60 (0.30), residues: 300 loop : -0.51 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.003 0.000 HIS A 188 PHE 0.009 0.001 PHE B 241 TYR 0.016 0.001 TYR S 190 ARG 0.015 0.001 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 186 time to evaluate : 1.080 Fit side-chains REVERT: A 270 LYS cc_start: 0.8020 (mtmm) cc_final: 0.7727 (mttm) REVERT: A 337 ASP cc_start: 0.7617 (m-30) cc_final: 0.7298 (m-30) REVERT: B 158 VAL cc_start: 0.8692 (p) cc_final: 0.8478 (p) REVERT: B 254 ASP cc_start: 0.6893 (t70) cc_final: 0.6576 (t70) REVERT: B 308 LEU cc_start: 0.8680 (mt) cc_final: 0.8444 (mp) REVERT: S 38 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7659 (ptt180) REVERT: R 146 ILE cc_start: 0.6780 (OUTLIER) cc_final: 0.6405 (mp) outliers start: 19 outliers final: 12 residues processed: 194 average time/residue: 1.3041 time to fit residues: 268.2344 Evaluate side-chains 201 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 187 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 111 optimal weight: 0.4980 chunk 102 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 70 optimal weight: 0.4980 chunk 94 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9319 Z= 0.184 Angle : 0.502 8.914 12610 Z= 0.273 Chirality : 0.042 0.185 1412 Planarity : 0.004 0.060 1594 Dihedral : 5.068 48.613 1290 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.61 % Allowed : 18.69 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.75 (0.25), residues: 1137 helix: 1.65 (0.27), residues: 390 sheet: 0.55 (0.30), residues: 301 loop : -0.52 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.004 0.001 HIS A 188 PHE 0.009 0.001 PHE R 117 TYR 0.021 0.001 TYR S 190 ARG 0.007 0.000 ARG B 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 192 time to evaluate : 0.970 Fit side-chains REVERT: A 270 LYS cc_start: 0.8033 (mtmm) cc_final: 0.7748 (mttm) REVERT: A 337 ASP cc_start: 0.7616 (m-30) cc_final: 0.7351 (m-30) REVERT: B 158 VAL cc_start: 0.8715 (p) cc_final: 0.8500 (p) REVERT: B 254 ASP cc_start: 0.6911 (t70) cc_final: 0.6582 (t70) REVERT: B 308 LEU cc_start: 0.8707 (mt) cc_final: 0.8461 (mp) REVERT: S 38 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7665 (ptt180) REVERT: R 146 ILE cc_start: 0.6808 (OUTLIER) cc_final: 0.6431 (mp) REVERT: R 212 ILE cc_start: 0.7275 (OUTLIER) cc_final: 0.6990 (mm) outliers start: 16 outliers final: 11 residues processed: 199 average time/residue: 1.2792 time to fit residues: 270.2625 Evaluate side-chains 202 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 188 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 212 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 78 optimal weight: 0.0770 chunk 5 optimal weight: 0.0870 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.147494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.125720 restraints weight = 12055.515| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.05 r_work: 0.3503 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9319 Z= 0.164 Angle : 0.493 9.079 12610 Z= 0.269 Chirality : 0.042 0.176 1412 Planarity : 0.004 0.060 1594 Dihedral : 4.975 47.636 1290 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.61 % Allowed : 18.99 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.77 (0.25), residues: 1137 helix: 1.66 (0.27), residues: 391 sheet: 0.54 (0.30), residues: 301 loop : -0.49 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.003 0.001 HIS A 188 PHE 0.008 0.001 PHE B 241 TYR 0.021 0.001 TYR R 284 ARG 0.014 0.000 ARG R 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4480.21 seconds wall clock time: 79 minutes 6.83 seconds (4746.83 seconds total)