Starting phenix.real_space_refine on Wed Feb 14 07:31:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hn8_34908/02_2024/8hn8_34908_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hn8_34908/02_2024/8hn8_34908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hn8_34908/02_2024/8hn8_34908.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hn8_34908/02_2024/8hn8_34908.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hn8_34908/02_2024/8hn8_34908_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hn8_34908/02_2024/8hn8_34908_neut_updated.pdb" } resolution = 3.0 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= -0.006 sd= 0.162 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 59 5.16 5 C 5673 2.51 5 N 1489 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8860 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2280 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 10, 'TRANS': 265} Chain breaks: 1 Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.21, per 1000 atoms: 0.59 Number of scatterers: 8860 At special positions: 0 Unit cell: (94.64, 122.72, 131.04, 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 59 16.00 O 1639 8.00 N 1489 7.00 C 5673 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 87 " - pdb=" SG CYS R 164 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 3.33 Conformation dependent library (CDL) restraints added in 1.8 seconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 13 sheets defined 35.2% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.806A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 50 removed outlier: 3.507A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 46 through 50' 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 279 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 300 through 310 removed outlier: 3.788A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.527A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.707A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) 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 'R' and resid 14 through 42 Processing helix chain 'R' and resid 49 through 77 removed outlier: 5.598A pdb=" N ILE R 69 " --> pdb=" O GLY R 65 " (cutoff:3.500A) Proline residue: R 70 - end of helix Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 86 through 117 Processing helix chain 'R' and resid 119 through 124 removed outlier: 3.684A pdb=" N THR R 124 " --> pdb=" O VAL R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 157 removed outlier: 3.524A pdb=" N VAL R 146 " --> pdb=" O LEU R 142 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASN R 147 " --> pdb=" O ALA R 143 " (cutoff:3.500A) Proline residue: R 149 - end of helix removed outlier: 4.822A pdb=" N SER R 156 " --> pdb=" O LEU R 152 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N TRP R 157 " --> pdb=" O VAL R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 204 removed outlier: 5.302A pdb=" N VAL R 185 " --> pdb=" O LEU R 181 " (cutoff:3.500A) Proline residue: R 186 - end of helix removed outlier: 4.038A pdb=" N ILE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR R 198 " --> pdb=" O ASN R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 328 removed outlier: 3.541A pdb=" N LEU R 308 " --> pdb=" O SER R 304 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE R 312 " --> pdb=" O LEU R 308 " (cutoff:3.500A) Proline residue: R 318 - end of helix removed outlier: 3.792A pdb=" N ILE R 324 " --> pdb=" O SER R 320 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE R 328 " --> pdb=" O ILE R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 357 removed outlier: 3.525A pdb=" N PHE R 344 " --> pdb=" O TYR R 340 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP R 345 " --> pdb=" O ARG R 341 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN R 347 " --> pdb=" O ALA R 343 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TRP R 348 " --> pdb=" O PHE R 344 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN R 350 " --> pdb=" O LEU R 346 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER R 351 " --> pdb=" O GLN R 347 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE R 352 " --> pdb=" O TRP R 348 " (cutoff:3.500A) Proline residue: R 355 - end of helix Processing helix chain 'R' and resid 365 through 373 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 321 removed outlier: 7.053A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.982A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.866A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.341A 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: 6.814A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.447A 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: 6.955A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.117A 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: 6.810A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.930A 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: 6.829A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.617A 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: 6.924A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.519A 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: 5.454A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.974A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'S' and resid 143 through 148 Processing sheet with id= M, first strand: chain 'S' and resid 214 through 219 removed outlier: 3.649A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1104 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: 2.67 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1432 1.32 - 1.44: 2575 1.44 - 1.57: 4970 1.57 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 9062 Sorted by residual: bond pdb=" CG HSM R 401 " pdb=" ND1 HSM R 401 " ideal model delta sigma weight residual 1.383 1.258 0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" CD2 HSM R 401 " pdb=" NE2 HSM R 401 " ideal model delta sigma weight residual 1.376 1.293 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C LEU R 301 " pdb=" O LEU R 301 " ideal model delta sigma weight residual 1.236 1.195 0.041 1.17e-02 7.31e+03 1.21e+01 bond pdb=" CA ALA R 298 " pdb=" CB ALA R 298 " ideal model delta sigma weight residual 1.528 1.475 0.053 1.59e-02 3.96e+03 1.12e+01 bond pdb=" N ALA R 298 " pdb=" CA ALA R 298 " ideal model delta sigma weight residual 1.459 1.422 0.037 1.23e-02 6.61e+03 8.92e+00 ... (remaining 9057 not shown) Histogram of bond angle deviations from ideal: 100.15 - 106.93: 201 106.93 - 113.70: 4971 113.70 - 120.47: 3428 120.47 - 127.24: 3572 127.24 - 134.01: 101 Bond angle restraints: 12273 Sorted by residual: angle pdb=" N LEU R 293 " pdb=" CA LEU R 293 " pdb=" C LEU R 293 " ideal model delta sigma weight residual 111.28 104.04 7.24 1.09e+00 8.42e-01 4.41e+01 angle pdb=" CA LEU R 301 " pdb=" C LEU R 301 " pdb=" N ALA R 302 " ideal model delta sigma weight residual 117.04 122.25 -5.21 1.24e+00 6.50e-01 1.76e+01 angle pdb=" C LEU R 295 " pdb=" N LEU R 296 " pdb=" CA LEU R 296 " ideal model delta sigma weight residual 120.28 115.25 5.03 1.34e+00 5.57e-01 1.41e+01 angle pdb=" N ALA S 92 " pdb=" CA ALA S 92 " pdb=" C ALA S 92 " ideal model delta sigma weight residual 108.14 113.31 -5.17 1.52e+00 4.33e-01 1.16e+01 angle pdb=" C LYS B 280 " pdb=" N SER B 281 " pdb=" CA SER B 281 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 ... (remaining 12268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 4845 17.54 - 35.07: 414 35.07 - 52.61: 53 52.61 - 70.15: 14 70.15 - 87.69: 11 Dihedral angle restraints: 5337 sinusoidal: 2082 harmonic: 3255 Sorted by residual: dihedral pdb=" CB CYS R 87 " pdb=" SG CYS R 87 " pdb=" SG CYS R 164 " pdb=" CB CYS R 164 " ideal model delta sinusoidal sigma weight residual -86.00 -160.93 74.93 1 1.00e+01 1.00e-02 7.10e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 158.56 21.44 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CB GLU R 165 " pdb=" CG GLU R 165 " pdb=" CD GLU R 165 " pdb=" OE1 GLU R 165 " ideal model delta sinusoidal sigma weight residual 0.00 87.69 -87.69 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 5334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 941 0.038 - 0.076: 321 0.076 - 0.115: 88 0.115 - 0.153: 18 0.153 - 0.191: 4 Chirality restraints: 1372 Sorted by residual: chirality pdb=" CA LEU R 296 " pdb=" N LEU R 296 " pdb=" C LEU R 296 " pdb=" CB LEU R 296 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CA ARG R 299 " pdb=" N ARG R 299 " pdb=" C ARG R 299 " pdb=" CB ARG R 299 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CG LEU R 293 " pdb=" CB LEU R 293 " pdb=" CD1 LEU R 293 " pdb=" CD2 LEU R 293 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 1369 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO G 49 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 301 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.36e+00 pdb=" C LEU R 301 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU R 301 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA R 302 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG R 334 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.94e+00 pdb=" N PRO R 335 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO R 335 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 335 " 0.020 5.00e-02 4.00e+02 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1328 2.76 - 3.30: 8068 3.30 - 3.83: 13971 3.83 - 4.37: 16442 4.37 - 4.90: 29849 Nonbonded interactions: 69658 Sorted by model distance: nonbonded pdb=" O ARG B 22 " pdb=" NE2 GLN B 259 " model vdw 2.225 2.520 nonbonded pdb=" OG SER S 134 " pdb=" OE1 GLU S 234 " model vdw 2.244 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.262 2.440 nonbonded pdb=" O CYS A 254 " pdb=" NZ LYS A 317 " model vdw 2.328 2.520 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.336 2.440 ... (remaining 69653 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: 1.050 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: 4.010 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.080 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:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 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 : 0.003 0.125 9062 Z= 0.217 Angle : 0.590 7.382 12273 Z= 0.349 Chirality : 0.042 0.191 1372 Planarity : 0.003 0.041 1543 Dihedral : 13.370 87.685 3228 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.41 % Allowed : 0.21 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1102 helix: 1.69 (0.28), residues: 383 sheet: 0.46 (0.31), residues: 280 loop : -0.87 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.014 0.001 PHE R 169 TYR 0.014 0.001 TYR S 178 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 1.023 Fit side-chains REVERT: A 309 ASP cc_start: 0.7096 (m-30) cc_final: 0.6716 (m-30) REVERT: R 125 GLN cc_start: 0.6974 (tt0) cc_final: 0.6418 (tt0) REVERT: R 297 ARG cc_start: 0.4644 (OUTLIER) cc_final: 0.4287 (mtt180) outliers start: 4 outliers final: 1 residues processed: 145 average time/residue: 1.1151 time to fit residues: 173.6458 Evaluate side-chains 106 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain R residue 297 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9062 Z= 0.223 Angle : 0.515 6.640 12273 Z= 0.272 Chirality : 0.043 0.202 1372 Planarity : 0.004 0.043 1543 Dihedral : 5.224 59.658 1220 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.18 % Allowed : 8.40 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.25), residues: 1102 helix: 1.86 (0.28), residues: 385 sheet: 0.28 (0.30), residues: 283 loop : -0.91 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.015 0.001 PHE R 322 TYR 0.021 0.001 TYR S 178 ARG 0.005 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 1.043 Fit side-chains REVERT: A 309 ASP cc_start: 0.7040 (m-30) cc_final: 0.6625 (m-30) REVERT: A 354 PHE cc_start: 0.8164 (t80) cc_final: 0.7884 (t80) REVERT: B 217 MET cc_start: 0.8106 (pmm) cc_final: 0.7726 (ppp) REVERT: B 268 ASN cc_start: 0.8107 (m110) cc_final: 0.7869 (m110) REVERT: R 125 GLN cc_start: 0.7013 (tt0) cc_final: 0.6364 (tt0) REVERT: R 297 ARG cc_start: 0.4731 (OUTLIER) cc_final: 0.4095 (mtt180) REVERT: S 11 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7909 (tt) outliers start: 21 outliers final: 9 residues processed: 121 average time/residue: 1.1406 time to fit residues: 148.1733 Evaluate side-chains 118 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.2980 chunk 30 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 20.0000 chunk 107 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9062 Z= 0.158 Angle : 0.474 6.177 12273 Z= 0.249 Chirality : 0.041 0.196 1372 Planarity : 0.003 0.040 1543 Dihedral : 4.821 59.796 1218 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.07 % Allowed : 10.06 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.67 (0.25), residues: 1102 helix: 2.02 (0.27), residues: 386 sheet: 0.24 (0.30), residues: 285 loop : -0.85 (0.28), residues: 431 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 0.010 0.001 PHE S 27 TYR 0.017 0.001 TYR S 178 ARG 0.005 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 1.012 Fit side-chains REVERT: A 252 SER cc_start: 0.7336 (m) cc_final: 0.7106 (m) REVERT: A 309 ASP cc_start: 0.7015 (m-30) cc_final: 0.6617 (m-30) REVERT: B 215 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: R 125 GLN cc_start: 0.7021 (tt0) cc_final: 0.6264 (tt0) REVERT: R 150 MET cc_start: 0.6889 (mmm) cc_final: 0.6617 (tpt) REVERT: R 297 ARG cc_start: 0.4597 (OUTLIER) cc_final: 0.4074 (mtt180) REVERT: S 11 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7890 (tt) outliers start: 20 outliers final: 9 residues processed: 122 average time/residue: 1.0761 time to fit residues: 141.6858 Evaluate side-chains 123 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 86 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9062 Z= 0.322 Angle : 0.558 6.352 12273 Z= 0.296 Chirality : 0.044 0.212 1372 Planarity : 0.004 0.043 1543 Dihedral : 4.897 56.741 1218 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.22 % Allowed : 10.89 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.40 (0.25), residues: 1102 helix: 1.75 (0.27), residues: 391 sheet: 0.09 (0.30), residues: 285 loop : -0.98 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.002 PHE S 27 TYR 0.026 0.002 TYR S 178 ARG 0.005 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 115 time to evaluate : 0.922 Fit side-chains REVERT: A 252 SER cc_start: 0.7460 (m) cc_final: 0.7243 (m) REVERT: A 309 ASP cc_start: 0.7028 (m-30) cc_final: 0.6600 (m-30) REVERT: B 197 ARG cc_start: 0.7532 (ttm-80) cc_final: 0.6803 (mtp-110) REVERT: R 297 ARG cc_start: 0.4716 (OUTLIER) cc_final: 0.4239 (mtt180) REVERT: R 322 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7201 (m-80) REVERT: S 11 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7901 (tt) outliers start: 31 outliers final: 14 residues processed: 133 average time/residue: 1.0290 time to fit residues: 147.8669 Evaluate side-chains 125 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9062 Z= 0.201 Angle : 0.497 6.553 12273 Z= 0.263 Chirality : 0.042 0.178 1372 Planarity : 0.003 0.040 1543 Dihedral : 4.672 59.041 1218 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.80 % Allowed : 12.66 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.47 (0.25), residues: 1102 helix: 1.79 (0.27), residues: 395 sheet: 0.15 (0.30), residues: 285 loop : -0.97 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE S 27 TYR 0.019 0.001 TYR S 178 ARG 0.005 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 0.942 Fit side-chains REVERT: A 198 MET cc_start: 0.8558 (ttm) cc_final: 0.8322 (ttm) REVERT: A 252 SER cc_start: 0.7476 (m) cc_final: 0.7248 (m) REVERT: A 309 ASP cc_start: 0.7022 (m-30) cc_final: 0.6580 (m-30) REVERT: B 197 ARG cc_start: 0.7478 (ttm-80) cc_final: 0.6707 (mtp-110) REVERT: B 268 ASN cc_start: 0.8244 (m110) cc_final: 0.8016 (m110) REVERT: R 30 MET cc_start: 0.6112 (OUTLIER) cc_final: 0.5859 (mmt) REVERT: R 125 GLN cc_start: 0.7284 (tt0) cc_final: 0.6912 (tt0) REVERT: R 297 ARG cc_start: 0.4769 (OUTLIER) cc_final: 0.4313 (mtt180) REVERT: R 322 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7175 (m-80) REVERT: S 11 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7886 (tt) outliers start: 27 outliers final: 13 residues processed: 132 average time/residue: 1.0651 time to fit residues: 151.7337 Evaluate side-chains 130 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.0970 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 101 optimal weight: 0.0370 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** R 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9062 Z= 0.138 Angle : 0.465 6.826 12273 Z= 0.243 Chirality : 0.041 0.196 1372 Planarity : 0.003 0.038 1543 Dihedral : 4.403 59.371 1218 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.70 % Allowed : 13.28 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.70 (0.26), residues: 1102 helix: 2.09 (0.27), residues: 388 sheet: 0.22 (0.30), residues: 287 loop : -0.88 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.011 0.001 PHE S 27 TYR 0.015 0.001 TYR S 178 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 1.088 Fit side-chains REVERT: A 198 MET cc_start: 0.8547 (ttm) cc_final: 0.8303 (ttm) REVERT: A 252 SER cc_start: 0.7478 (m) cc_final: 0.7257 (m) REVERT: A 309 ASP cc_start: 0.7038 (m-30) cc_final: 0.6622 (m-30) REVERT: B 197 ARG cc_start: 0.7384 (ttm-80) cc_final: 0.6694 (mtt-85) REVERT: B 268 ASN cc_start: 0.8120 (m110) cc_final: 0.7886 (m110) REVERT: R 30 MET cc_start: 0.5931 (tpp) cc_final: 0.5691 (mmt) REVERT: R 125 GLN cc_start: 0.7181 (tt0) cc_final: 0.6811 (tt0) REVERT: R 297 ARG cc_start: 0.4880 (OUTLIER) cc_final: 0.4311 (mtt180) REVERT: R 322 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.7046 (m-80) REVERT: S 11 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7882 (tt) outliers start: 26 outliers final: 14 residues processed: 128 average time/residue: 1.0801 time to fit residues: 150.3062 Evaluate side-chains 129 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 0.0170 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 41 optimal weight: 2.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** R 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9062 Z= 0.164 Angle : 0.475 6.642 12273 Z= 0.250 Chirality : 0.041 0.208 1372 Planarity : 0.003 0.039 1543 Dihedral : 4.362 58.920 1218 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.80 % Allowed : 13.69 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.26), residues: 1102 helix: 2.13 (0.27), residues: 388 sheet: 0.22 (0.30), residues: 287 loop : -0.85 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 362 PHE 0.011 0.001 PHE S 27 TYR 0.018 0.001 TYR S 178 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 0.936 Fit side-chains REVERT: A 198 MET cc_start: 0.8524 (ttm) cc_final: 0.8269 (ttm) REVERT: A 252 SER cc_start: 0.7653 (m) cc_final: 0.7422 (m) REVERT: A 309 ASP cc_start: 0.7040 (m-30) cc_final: 0.6624 (m-30) REVERT: B 197 ARG cc_start: 0.7383 (ttm-80) cc_final: 0.6683 (mtt-85) REVERT: B 234 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8592 (m-80) REVERT: B 268 ASN cc_start: 0.8135 (m110) cc_final: 0.7896 (m110) REVERT: R 30 MET cc_start: 0.5830 (tpp) cc_final: 0.5589 (mmt) REVERT: R 125 GLN cc_start: 0.7194 (tt0) cc_final: 0.6862 (tt0) REVERT: R 297 ARG cc_start: 0.4886 (OUTLIER) cc_final: 0.4326 (mtt180) REVERT: R 322 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7079 (m-80) REVERT: S 11 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7880 (tt) REVERT: S 150 SER cc_start: 0.8791 (t) cc_final: 0.8222 (p) outliers start: 27 outliers final: 15 residues processed: 128 average time/residue: 1.0594 time to fit residues: 146.5994 Evaluate side-chains 126 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 100 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** R 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9062 Z= 0.205 Angle : 0.493 6.136 12273 Z= 0.260 Chirality : 0.042 0.224 1372 Planarity : 0.003 0.040 1543 Dihedral : 4.407 58.345 1218 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.80 % Allowed : 13.80 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.66 (0.26), residues: 1102 helix: 2.07 (0.27), residues: 388 sheet: 0.19 (0.30), residues: 287 loop : -0.89 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.011 0.001 PHE S 27 TYR 0.020 0.001 TYR S 178 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 110 time to evaluate : 1.051 Fit side-chains REVERT: A 198 MET cc_start: 0.8541 (ttm) cc_final: 0.8290 (ttm) REVERT: A 252 SER cc_start: 0.7658 (m) cc_final: 0.7428 (m) REVERT: A 309 ASP cc_start: 0.7039 (m-30) cc_final: 0.6623 (m-30) REVERT: B 197 ARG cc_start: 0.7420 (ttm-80) cc_final: 0.6705 (mtt-85) REVERT: B 215 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7377 (mt-10) REVERT: B 217 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7795 (ppp) REVERT: B 234 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8608 (m-80) REVERT: B 268 ASN cc_start: 0.8153 (m110) cc_final: 0.7918 (m110) REVERT: R 30 MET cc_start: 0.5908 (tpp) cc_final: 0.5668 (mmt) REVERT: R 125 GLN cc_start: 0.7281 (tt0) cc_final: 0.6946 (tt0) REVERT: R 297 ARG cc_start: 0.4835 (OUTLIER) cc_final: 0.4299 (mtt180) REVERT: R 322 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7154 (m-80) REVERT: S 11 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7868 (tt) REVERT: S 150 SER cc_start: 0.8788 (t) cc_final: 0.8182 (p) outliers start: 27 outliers final: 17 residues processed: 128 average time/residue: 1.0235 time to fit residues: 141.7353 Evaluate side-chains 131 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 108 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 chunk 64 optimal weight: 0.0030 chunk 103 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9062 Z= 0.146 Angle : 0.463 5.874 12273 Z= 0.244 Chirality : 0.041 0.219 1372 Planarity : 0.003 0.039 1543 Dihedral : 4.271 57.451 1218 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.59 % Allowed : 14.42 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.74 (0.26), residues: 1102 helix: 2.07 (0.27), residues: 395 sheet: 0.26 (0.30), residues: 287 loop : -0.86 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS R 362 PHE 0.010 0.001 PHE S 27 TYR 0.015 0.001 TYR S 178 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 0.950 Fit side-chains REVERT: A 198 MET cc_start: 0.8531 (ttm) cc_final: 0.8279 (ttm) REVERT: A 252 SER cc_start: 0.7658 (m) cc_final: 0.7431 (m) REVERT: A 309 ASP cc_start: 0.7036 (m-30) cc_final: 0.6618 (m-30) REVERT: B 197 ARG cc_start: 0.7381 (ttm-80) cc_final: 0.6654 (mtt-85) REVERT: B 215 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7316 (mt-10) REVERT: B 217 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7880 (ppp) REVERT: B 234 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8594 (m-80) REVERT: B 268 ASN cc_start: 0.8152 (m110) cc_final: 0.7909 (m110) REVERT: R 30 MET cc_start: 0.5663 (tpp) cc_final: 0.5430 (mmt) REVERT: R 125 GLN cc_start: 0.7198 (tt0) cc_final: 0.6887 (tt0) REVERT: R 297 ARG cc_start: 0.4873 (OUTLIER) cc_final: 0.4283 (mtt180) REVERT: R 322 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7124 (m-80) REVERT: S 11 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7860 (tt) REVERT: S 150 SER cc_start: 0.8765 (t) cc_final: 0.8150 (p) outliers start: 25 outliers final: 14 residues processed: 129 average time/residue: 1.0413 time to fit residues: 144.9480 Evaluate side-chains 128 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 99 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 8 optimal weight: 0.2980 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** R 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9062 Z= 0.151 Angle : 0.467 5.599 12273 Z= 0.246 Chirality : 0.041 0.245 1372 Planarity : 0.003 0.039 1543 Dihedral : 4.234 56.825 1218 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.39 % Allowed : 14.73 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.26), residues: 1102 helix: 2.18 (0.27), residues: 388 sheet: 0.28 (0.30), residues: 287 loop : -0.83 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 362 PHE 0.010 0.001 PHE S 27 TYR 0.017 0.001 TYR S 178 ARG 0.007 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 0.936 Fit side-chains REVERT: A 198 MET cc_start: 0.8526 (ttm) cc_final: 0.8275 (ttm) REVERT: A 252 SER cc_start: 0.7659 (m) cc_final: 0.7436 (m) REVERT: A 309 ASP cc_start: 0.7039 (m-30) cc_final: 0.6622 (m-30) REVERT: B 197 ARG cc_start: 0.7376 (ttm-80) cc_final: 0.6651 (mtt-85) REVERT: B 215 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7327 (mt-10) REVERT: B 217 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7883 (ppp) REVERT: B 234 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8583 (m-80) REVERT: B 268 ASN cc_start: 0.8167 (m110) cc_final: 0.7927 (m110) REVERT: R 30 MET cc_start: 0.5674 (tpp) cc_final: 0.5415 (mmt) REVERT: R 125 GLN cc_start: 0.7202 (tt0) cc_final: 0.6888 (tt0) REVERT: R 297 ARG cc_start: 0.4773 (OUTLIER) cc_final: 0.4239 (mtt180) REVERT: R 322 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7109 (m-80) REVERT: S 11 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7864 (tt) REVERT: S 150 SER cc_start: 0.8800 (t) cc_final: 0.8230 (p) outliers start: 23 outliers final: 15 residues processed: 130 average time/residue: 1.0835 time to fit residues: 151.8815 Evaluate side-chains 131 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 76 optimal weight: 0.8980 chunk 4 optimal weight: 0.0040 chunk 62 optimal weight: 0.9980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.155611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.118363 restraints weight = 10214.401| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.21 r_work: 0.3234 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9062 Z= 0.140 Angle : 0.458 5.464 12273 Z= 0.241 Chirality : 0.041 0.239 1372 Planarity : 0.003 0.038 1543 Dihedral : 4.147 55.043 1218 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.28 % Allowed : 14.83 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.86 (0.26), residues: 1102 helix: 2.26 (0.27), residues: 386 sheet: 0.32 (0.30), residues: 287 loop : -0.81 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS R 362 PHE 0.010 0.001 PHE S 27 TYR 0.015 0.001 TYR S 178 ARG 0.007 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3250.93 seconds wall clock time: 58 minutes 49.04 seconds (3529.04 seconds total)