Starting phenix.real_space_refine on Thu Jan 18 15:21:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yac_33708/01_2024/7yac_33708_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yac_33708/01_2024/7yac_33708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yac_33708/01_2024/7yac_33708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yac_33708/01_2024/7yac_33708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yac_33708/01_2024/7yac_33708_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yac_33708/01_2024/7yac_33708_updated.pdb" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians S 68 5.16 5 C 5703 2.51 5 N 1508 2.21 5 O 1656 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "S GLU 42": "OE1" <-> "OE2" Residue "S GLU 89": "OE1" <-> "OE2" Residue "S GLU 153": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8937 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1817 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 474 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 4, 'TRANS': 56} Chain: "E" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2218 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 269} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'IUD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.22, per 1000 atoms: 0.58 Number of scatterers: 8937 At special positions: 0 Unit cell: (125.8, 98.6, 123.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 F 2 9.00 O 1656 8.00 N 1508 7.00 C 5703 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.40 Conformation dependent library (CDL) restraints added in 1.8 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 14 sheets defined 33.3% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.687A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (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 280 removed outlier: 3.636A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 286 Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 329 through 351 removed outlier: 4.379A pdb=" N GLN A 333 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N PHE A 334 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS A 351 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 22 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.471A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 21 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'E' and resid 43 through 71 Processing helix chain 'E' and resid 77 through 103 removed outlier: 3.517A pdb=" N LEU E 91 " --> pdb=" O ILE E 87 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET E 93 " --> pdb=" O ASP E 89 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU E 94 " --> pdb=" O GLU E 90 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU E 96 " --> pdb=" O PHE E 92 " (cutoff:3.500A) Proline residue: E 97 - end of helix removed outlier: 3.835A pdb=" N MET E 101 " --> pdb=" O PRO E 97 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN E 102 " --> pdb=" O PHE E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 145 Processing helix chain 'E' and resid 150 through 155 Processing helix chain 'E' and resid 158 through 178 Proline residue: E 176 - end of helix Processing helix chain 'E' and resid 201 through 216 removed outlier: 4.302A pdb=" N THR E 206 " --> pdb=" O GLY E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 241 removed outlier: 3.680A pdb=" N THR E 222 " --> pdb=" O LEU E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 281 removed outlier: 3.540A pdb=" N LYS E 252 " --> pdb=" O LYS E 248 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS E 253 " --> pdb=" O LYS E 249 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL E 254 " --> pdb=" O SER E 250 " (cutoff:3.500A) Proline residue: E 271 - end of helix Processing helix chain 'E' and resid 288 through 312 removed outlier: 3.933A pdb=" N ASN E 304 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N SER E 305 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N CYS E 306 " --> pdb=" O TYR E 302 " (cutoff:3.500A) Proline residue: E 309 - end of helix Processing helix chain 'E' and resid 318 through 321 No H-bonds generated for 'chain 'E' and resid 318 through 321' 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 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.504A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.858A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.580A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.939A 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: 6.549A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 220 through 222 removed outlier: 3.625A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.754A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.680A 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 277 removed outlier: 6.639A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.671A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.607A 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 removed outlier: 3.649A pdb=" N PHE S 80 " --> pdb=" O SER S 71 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 10 through 12 Processing sheet with id= K, first strand: chain 'S' and resid 95 through 99 removed outlier: 3.586A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.979A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'S' and resid 155 through 159 removed outlier: 3.527A pdb=" N VAL S 155 " --> pdb=" O ILE S 216 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N CYS S 159 " --> pdb=" O PHE S 212 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE S 212 " --> pdb=" O CYS S 159 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S' and resid 226 through 231 removed outlier: 5.966A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 1002 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: 2.50 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1438 1.27 - 1.41: 2313 1.41 - 1.55: 5267 1.55 - 1.68: 8 1.68 - 1.82: 100 Bond restraints: 9126 Sorted by residual: bond pdb=" C08 IUD E 401 " pdb=" N03 IUD E 401 " ideal model delta sigma weight residual 1.386 1.521 -0.135 2.00e-02 2.50e+03 4.57e+01 bond pdb=" C30 IUD E 401 " pdb=" C33 IUD E 401 " ideal model delta sigma weight residual 1.423 1.525 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C02 IUD E 401 " pdb=" N03 IUD E 401 " ideal model delta sigma weight residual 1.453 1.535 -0.082 2.00e-02 2.50e+03 1.66e+01 bond pdb=" C04 IUD E 401 " pdb=" N03 IUD E 401 " ideal model delta sigma weight residual 1.457 1.534 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C01 IUD E 401 " pdb=" C06 IUD E 401 " ideal model delta sigma weight residual 1.534 1.461 0.073 2.00e-02 2.50e+03 1.34e+01 ... (remaining 9121 not shown) Histogram of bond angle deviations from ideal: 98.94 - 115.14: 5711 115.14 - 131.33: 6621 131.33 - 147.52: 22 147.52 - 163.71: 0 163.71 - 179.91: 1 Bond angle restraints: 12355 Sorted by residual: angle pdb=" N THR B 165 " pdb=" CA THR B 165 " pdb=" C THR B 165 " ideal model delta sigma weight residual 109.06 115.44 -6.38 1.70e+00 3.46e-01 1.41e+01 angle pdb=" N ARG B 68 " pdb=" CA ARG B 68 " pdb=" C ARG B 68 " ideal model delta sigma weight residual 114.56 110.33 4.23 1.27e+00 6.20e-01 1.11e+01 angle pdb=" CB MET E 178 " pdb=" CG MET E 178 " pdb=" SD MET E 178 " ideal model delta sigma weight residual 112.70 122.53 -9.83 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CA MET E 178 " pdb=" CB MET E 178 " pdb=" CG MET E 178 " ideal model delta sigma weight residual 114.10 120.00 -5.90 2.00e+00 2.50e-01 8.69e+00 angle pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta sigma weight residual 121.54 126.94 -5.40 1.91e+00 2.74e-01 7.99e+00 ... (remaining 12350 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 4854 17.59 - 35.18: 448 35.18 - 52.76: 100 52.76 - 70.35: 14 70.35 - 87.94: 5 Dihedral angle restraints: 5421 sinusoidal: 2121 harmonic: 3300 Sorted by residual: dihedral pdb=" CA ARG E 155 " pdb=" C ARG E 155 " pdb=" N PRO E 156 " pdb=" CA PRO E 156 " ideal model delta harmonic sigma weight residual -180.00 -161.46 -18.54 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ASN A 269 " pdb=" C ASN A 269 " pdb=" N LYS A 270 " pdb=" CA LYS A 270 " ideal model delta harmonic sigma weight residual 180.00 161.98 18.02 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA LEU E 105 " pdb=" C LEU E 105 " pdb=" N VAL E 106 " pdb=" CA VAL E 106 " ideal model delta harmonic sigma weight residual -180.00 -163.82 -16.18 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 5418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 823 0.028 - 0.055: 355 0.055 - 0.083: 132 0.083 - 0.111: 64 0.111 - 0.138: 24 Chirality restraints: 1398 Sorted by residual: chirality pdb=" CA PRO E 309 " pdb=" N PRO E 309 " pdb=" C PRO E 309 " pdb=" CB PRO E 309 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CG LEU S 166 " pdb=" CB LEU S 166 " pdb=" CD1 LEU S 166 " pdb=" CD2 LEU S 166 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA VAL B 112 " pdb=" N VAL B 112 " pdb=" C VAL B 112 " pdb=" CB VAL B 112 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 1395 not shown) Planarity restraints: 1550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 308 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.26e+00 pdb=" N PRO E 309 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO E 309 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 309 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL S 147 " 0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO S 148 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO S 148 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO S 148 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR S 235 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO S 236 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO S 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO S 236 " 0.025 5.00e-02 4.00e+02 ... (remaining 1547 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1486 2.77 - 3.30: 8324 3.30 - 3.83: 13908 3.83 - 4.37: 15710 4.37 - 4.90: 28056 Nonbonded interactions: 67484 Sorted by model distance: nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.235 2.520 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.276 2.440 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.305 2.440 nonbonded pdb=" OE2 GLU A 186 " pdb=" NE2 HIS A 188 " model vdw 2.317 2.520 nonbonded pdb=" NE ARG B 137 " pdb=" O ILE B 171 " model vdw 2.322 2.520 ... (remaining 67479 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 3.960 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.340 Find NCS groups from input model: 0.270 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 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 0.135 9126 Z= 0.246 Angle : 0.590 9.833 12355 Z= 0.320 Chirality : 0.040 0.138 1398 Planarity : 0.004 0.057 1550 Dihedral : 14.304 87.937 3292 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.25), residues: 1126 helix: 1.68 (0.27), residues: 370 sheet: 0.15 (0.32), residues: 271 loop : -1.33 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.011 0.001 PHE S 177 TYR 0.014 0.001 TYR E 50 ARG 0.003 0.000 ARG S 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.129 Fit side-chains REVERT: C 21 MET cc_start: 0.5655 (ttt) cc_final: 0.5200 (tmm) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2267 time to fit residues: 50.7678 Evaluate side-chains 135 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN E 276 ASN E 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9126 Z= 0.174 Angle : 0.545 8.931 12355 Z= 0.289 Chirality : 0.042 0.140 1398 Planarity : 0.004 0.049 1550 Dihedral : 4.844 38.887 1253 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.54 % Allowed : 7.59 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1126 helix: 2.02 (0.27), residues: 359 sheet: 0.22 (0.33), residues: 268 loop : -1.41 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 PHE 0.018 0.001 PHE S 177 TYR 0.010 0.001 TYR E 50 ARG 0.002 0.000 ARG S 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 1.125 Fit side-chains REVERT: A 243 MET cc_start: 0.5911 (tmm) cc_final: 0.5619 (tmm) REVERT: C 21 MET cc_start: 0.6074 (ttt) cc_final: 0.5465 (tmm) REVERT: E 92 PHE cc_start: 0.6468 (OUTLIER) cc_final: 0.5771 (m-80) REVERT: E 153 TRP cc_start: 0.5205 (t60) cc_final: 0.4825 (t60) REVERT: E 178 MET cc_start: 0.6145 (tmm) cc_final: 0.5917 (tmm) REVERT: E 276 ASN cc_start: 0.6506 (m-40) cc_final: 0.6165 (m110) outliers start: 15 outliers final: 11 residues processed: 158 average time/residue: 0.2057 time to fit residues: 45.4607 Evaluate side-chains 144 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 91 optimal weight: 0.0470 chunk 101 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9126 Z= 0.140 Angle : 0.506 8.600 12355 Z= 0.269 Chirality : 0.041 0.141 1398 Planarity : 0.004 0.048 1550 Dihedral : 4.674 39.344 1253 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.95 % Allowed : 10.77 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1126 helix: 2.05 (0.27), residues: 360 sheet: 0.30 (0.33), residues: 263 loop : -1.36 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.015 0.001 PHE S 177 TYR 0.010 0.001 TYR E 50 ARG 0.004 0.000 ARG S 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 1.122 Fit side-chains REVERT: A 243 MET cc_start: 0.5798 (tmm) cc_final: 0.5555 (tmm) REVERT: C 31 SER cc_start: 0.7393 (t) cc_final: 0.7175 (m) REVERT: E 84 ASN cc_start: 0.8036 (t0) cc_final: 0.7686 (m-40) REVERT: E 92 PHE cc_start: 0.6645 (OUTLIER) cc_final: 0.5838 (m-80) REVERT: E 178 MET cc_start: 0.6001 (tmm) cc_final: 0.5584 (tmm) REVERT: S 38 ARG cc_start: 0.7582 (tpp80) cc_final: 0.7314 (ttm170) outliers start: 19 outliers final: 15 residues processed: 148 average time/residue: 0.2088 time to fit residues: 43.1629 Evaluate side-chains 148 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9126 Z= 0.291 Angle : 0.626 9.337 12355 Z= 0.334 Chirality : 0.045 0.166 1398 Planarity : 0.005 0.056 1550 Dihedral : 5.277 36.059 1253 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.20 % Rotamer: Outliers : 2.87 % Allowed : 13.33 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.25), residues: 1126 helix: 1.71 (0.27), residues: 361 sheet: 0.12 (0.32), residues: 270 loop : -1.56 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 99 HIS 0.004 0.001 HIS A 213 PHE 0.031 0.002 PHE S 177 TYR 0.016 0.002 TYR S 94 ARG 0.003 0.001 ARG E 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 133 time to evaluate : 1.063 Fit side-chains REVERT: B 267 ASP cc_start: 0.6046 (OUTLIER) cc_final: 0.5755 (t0) REVERT: C 21 MET cc_start: 0.6185 (ttt) cc_final: 0.5486 (tmm) REVERT: E 92 PHE cc_start: 0.7011 (OUTLIER) cc_final: 0.6157 (m-80) REVERT: E 178 MET cc_start: 0.6003 (tmm) cc_final: 0.5709 (tmm) REVERT: S 192 MET cc_start: 0.8518 (ppp) cc_final: 0.8026 (ptm) outliers start: 28 outliers final: 23 residues processed: 155 average time/residue: 0.2325 time to fit residues: 49.0691 Evaluate side-chains 149 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 chunk 93 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN E 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9126 Z= 0.186 Angle : 0.549 8.792 12355 Z= 0.291 Chirality : 0.042 0.142 1398 Planarity : 0.004 0.053 1550 Dihedral : 5.041 37.235 1253 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.97 % Allowed : 15.38 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.25), residues: 1126 helix: 1.70 (0.27), residues: 366 sheet: 0.05 (0.31), residues: 277 loop : -1.54 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS B 183 PHE 0.022 0.001 PHE S 177 TYR 0.008 0.001 TYR E 50 ARG 0.002 0.000 ARG E 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 1.065 Fit side-chains REVERT: C 21 MET cc_start: 0.6152 (ttt) cc_final: 0.5479 (tmm) REVERT: C 31 SER cc_start: 0.7442 (t) cc_final: 0.7165 (m) REVERT: E 92 PHE cc_start: 0.7027 (OUTLIER) cc_final: 0.6143 (m-80) REVERT: E 178 MET cc_start: 0.6075 (tmm) cc_final: 0.5717 (tmm) REVERT: S 39 GLN cc_start: 0.7137 (tm-30) cc_final: 0.6816 (tp-100) outliers start: 29 outliers final: 25 residues processed: 152 average time/residue: 0.2035 time to fit residues: 43.2997 Evaluate side-chains 154 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 194 ASN Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9126 Z= 0.240 Angle : 0.593 9.326 12355 Z= 0.314 Chirality : 0.043 0.152 1398 Planarity : 0.004 0.060 1550 Dihedral : 5.229 36.810 1253 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.38 % Allowed : 16.41 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1126 helix: 1.61 (0.27), residues: 366 sheet: -0.04 (0.31), residues: 276 loop : -1.61 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.026 0.002 PHE S 177 TYR 0.010 0.002 TYR S 94 ARG 0.004 0.000 ARG E 247 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 1.157 Fit side-chains REVERT: A 331 ASN cc_start: 0.7868 (m-40) cc_final: 0.7512 (t0) REVERT: C 21 MET cc_start: 0.6122 (ttt) cc_final: 0.5470 (tmm) REVERT: C 31 SER cc_start: 0.7486 (t) cc_final: 0.7187 (m) REVERT: E 92 PHE cc_start: 0.6990 (OUTLIER) cc_final: 0.6111 (m-80) REVERT: E 178 MET cc_start: 0.6022 (tmm) cc_final: 0.5607 (tmm) REVERT: S 192 MET cc_start: 0.8547 (ppp) cc_final: 0.8144 (ptm) outliers start: 33 outliers final: 30 residues processed: 158 average time/residue: 0.2266 time to fit residues: 48.8745 Evaluate side-chains 163 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 132 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 167 HIS Chi-restraints excluded: chain S residue 194 ASN Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 0.0370 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9126 Z= 0.246 Angle : 0.595 9.636 12355 Z= 0.315 Chirality : 0.044 0.153 1398 Planarity : 0.004 0.061 1550 Dihedral : 5.287 36.771 1253 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.49 % Allowed : 17.23 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.25), residues: 1126 helix: 1.55 (0.27), residues: 365 sheet: -0.07 (0.31), residues: 274 loop : -1.60 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.025 0.002 PHE S 177 TYR 0.010 0.002 TYR S 94 ARG 0.004 0.000 ARG E 247 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 134 time to evaluate : 1.086 Fit side-chains REVERT: A 331 ASN cc_start: 0.7879 (m-40) cc_final: 0.7536 (t0) REVERT: C 21 MET cc_start: 0.6084 (ttt) cc_final: 0.5411 (tmm) REVERT: E 92 PHE cc_start: 0.6974 (OUTLIER) cc_final: 0.6128 (m-80) REVERT: E 178 MET cc_start: 0.6004 (tmm) cc_final: 0.5121 (tmm) REVERT: S 192 MET cc_start: 0.8519 (ppp) cc_final: 0.8139 (ptm) outliers start: 34 outliers final: 31 residues processed: 158 average time/residue: 0.2185 time to fit residues: 47.1857 Evaluate side-chains 163 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 131 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 167 HIS Chi-restraints excluded: chain S residue 194 ASN Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9126 Z= 0.204 Angle : 0.572 9.739 12355 Z= 0.301 Chirality : 0.043 0.166 1398 Planarity : 0.004 0.057 1550 Dihedral : 5.173 37.683 1253 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.90 % Allowed : 17.13 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.25), residues: 1126 helix: 1.61 (0.27), residues: 365 sheet: -0.17 (0.31), residues: 280 loop : -1.47 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.021 0.001 PHE S 177 TYR 0.010 0.001 TYR A 230 ARG 0.003 0.000 ARG E 247 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 138 time to evaluate : 0.959 Fit side-chains REVERT: A 331 ASN cc_start: 0.7821 (m-40) cc_final: 0.7482 (t0) REVERT: B 119 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.8075 (m-40) REVERT: C 21 MET cc_start: 0.6096 (ttt) cc_final: 0.5432 (tmm) REVERT: E 92 PHE cc_start: 0.6972 (OUTLIER) cc_final: 0.6099 (m-80) REVERT: E 178 MET cc_start: 0.6073 (tmm) cc_final: 0.5183 (tmm) REVERT: S 39 GLN cc_start: 0.7321 (tm-30) cc_final: 0.6947 (tp-100) REVERT: S 192 MET cc_start: 0.8530 (ppp) cc_final: 0.8154 (ptm) outliers start: 38 outliers final: 34 residues processed: 165 average time/residue: 0.2192 time to fit residues: 49.4181 Evaluate side-chains 167 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 131 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 167 HIS Chi-restraints excluded: chain S residue 194 ASN Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 44 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9126 Z= 0.147 Angle : 0.532 9.784 12355 Z= 0.278 Chirality : 0.042 0.146 1398 Planarity : 0.004 0.053 1550 Dihedral : 4.859 39.076 1253 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.38 % Allowed : 18.26 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.25), residues: 1126 helix: 1.78 (0.27), residues: 364 sheet: -0.07 (0.31), residues: 276 loop : -1.41 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.015 0.001 PHE S 177 TYR 0.008 0.001 TYR A 230 ARG 0.003 0.000 ARG E 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 140 time to evaluate : 1.082 Fit side-chains REVERT: A 230 TYR cc_start: 0.5910 (t80) cc_final: 0.5518 (t80) REVERT: A 331 ASN cc_start: 0.7730 (m-40) cc_final: 0.7417 (t0) REVERT: B 119 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7901 (m-40) REVERT: C 21 MET cc_start: 0.6106 (ttt) cc_final: 0.5486 (tmm) REVERT: E 92 PHE cc_start: 0.6918 (OUTLIER) cc_final: 0.6003 (m-80) REVERT: E 178 MET cc_start: 0.6096 (tmm) cc_final: 0.5661 (tmm) REVERT: S 39 GLN cc_start: 0.7180 (tm-30) cc_final: 0.6889 (tp-100) REVERT: S 192 MET cc_start: 0.8528 (ppp) cc_final: 0.8055 (ptm) outliers start: 33 outliers final: 28 residues processed: 163 average time/residue: 0.2150 time to fit residues: 48.2081 Evaluate side-chains 162 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 132 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 194 ASN Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 112 optimal weight: 0.1980 chunk 103 optimal weight: 0.0470 chunk 89 optimal weight: 0.9990 chunk 9 optimal weight: 0.0370 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN E 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9126 Z= 0.121 Angle : 0.507 9.364 12355 Z= 0.264 Chirality : 0.041 0.151 1398 Planarity : 0.004 0.046 1550 Dihedral : 4.533 39.838 1253 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.26 % Allowed : 19.49 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1126 helix: 1.84 (0.27), residues: 364 sheet: 0.03 (0.31), residues: 270 loop : -1.32 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.001 0.000 HIS S 35 PHE 0.012 0.001 PHE S 177 TYR 0.007 0.001 TYR S 102 ARG 0.002 0.000 ARG E 247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 1.062 Fit side-chains REVERT: A 230 TYR cc_start: 0.5693 (t80) cc_final: 0.5385 (t80) REVERT: A 331 ASN cc_start: 0.7604 (m-40) cc_final: 0.7335 (t0) REVERT: B 45 MET cc_start: 0.7479 (mtm) cc_final: 0.7271 (mtt) REVERT: C 21 MET cc_start: 0.6149 (ttt) cc_final: 0.5508 (tmm) REVERT: E 92 PHE cc_start: 0.6853 (OUTLIER) cc_final: 0.5994 (m-80) REVERT: E 178 MET cc_start: 0.6026 (tmm) cc_final: 0.5686 (tmm) REVERT: S 39 GLN cc_start: 0.7204 (tm-30) cc_final: 0.6964 (tp-100) outliers start: 22 outliers final: 18 residues processed: 158 average time/residue: 0.2069 time to fit residues: 45.2982 Evaluate side-chains 149 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 194 ASN Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.0570 chunk 13 optimal weight: 0.0870 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 ASN S 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.184116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.129945 restraints weight = 11392.351| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.93 r_work: 0.3255 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9126 Z= 0.149 Angle : 0.533 9.503 12355 Z= 0.278 Chirality : 0.042 0.162 1398 Planarity : 0.004 0.050 1550 Dihedral : 4.593 38.092 1253 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.56 % Allowed : 19.28 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1126 helix: 1.89 (0.27), residues: 362 sheet: 0.04 (0.31), residues: 270 loop : -1.35 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 153 HIS 0.002 0.001 HIS B 142 PHE 0.018 0.001 PHE S 239 TYR 0.007 0.001 TYR E 50 ARG 0.002 0.000 ARG E 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2178.25 seconds wall clock time: 40 minutes 15.60 seconds (2415.60 seconds total)