Starting phenix.real_space_refine on Wed Feb 14 03:46:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e33_30975/02_2024/7e33_30975_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e33_30975/02_2024/7e33_30975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e33_30975/02_2024/7e33_30975.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e33_30975/02_2024/7e33_30975.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e33_30975/02_2024/7e33_30975_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e33_30975/02_2024/7e33_30975_neut_updated.pdb" } resolution = 2.9 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= 0.014 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 62 5.16 5 C 5446 2.51 5 N 1438 2.21 5 O 1592 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 "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "E GLU 153": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "R ARG 132": "NH1" <-> "NH2" Residue "R ARG 134": "NH1" <-> "NH2" Residue "R GLU 286": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8538 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1750 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2558 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain: "E" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1762 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain breaks: 1 Chain: "G" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 391 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 4, 'TRANS': 45} Chain: "R" Number of atoms: 2077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2077 Unusual residues: {'HVU': 1} Classifications: {'peptide': 257, 'undetermined': 1} Link IDs: {'PTRANS': 7, 'TRANS': 249, None: 1} Not linked: pdbres="LEU R 358 " pdbres="HVU R 501 " Chain breaks: 2 Time building chain proxies: 4.89, per 1000 atoms: 0.57 Number of scatterers: 8538 At special positions: 0 Unit cell: (107.635, 112.86, 114.95, 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 62 16.00 O 1592 8.00 N 1438 7.00 C 5446 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 173 " 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: 3.42 Conformation dependent library (CDL) restraints added in 1.7 seconds 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2038 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 12 sheets defined 36.0% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.595A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 212 through 217 removed outlier: 4.574A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.185A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) 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 296 through 310 Processing helix chain 'A' and resid 328 through 351 Processing helix chain 'B' and resid 9 through 25 removed outlier: 4.435A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'G' and resid 14 through 24 Processing helix chain 'G' and resid 30 through 47 removed outlier: 4.477A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 49 Processing helix chain 'R' and resid 51 through 53 No H-bonds generated for 'chain 'R' and resid 51 through 53' Processing helix chain 'R' and resid 56 through 74 Processing helix chain 'R' and resid 76 through 84 Processing helix chain 'R' and resid 92 through 125 removed outlier: 4.475A pdb=" N GLU R 96 " --> pdb=" O TYR R 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 133 removed outlier: 3.938A pdb=" N LYS R 133 " --> pdb=" O GLU R 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 129 through 133' Processing helix chain 'R' and resid 136 through 155 Processing helix chain 'R' and resid 180 through 190 Processing helix chain 'R' and resid 192 through 211 Processing helix chain 'R' and resid 284 through 315 Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 323 through 345 removed outlier: 4.087A pdb=" N ASN R 336 " --> pdb=" O LEU R 332 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N SER R 337 " --> pdb=" O GLY R 333 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU R 338 " --> pdb=" O TYR R 334 " (cutoff:3.500A) Proline residue: R 341 - end of helix Processing helix chain 'R' and resid 349 through 357 Processing sheet with id= A, first strand: chain 'A' and resid 263 through 269 removed outlier: 3.595A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.089A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.104A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.516A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.656A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.850A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.341A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.295A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR B 289 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.509A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.772A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 155 through 160 Processing sheet with id= L, first strand: chain 'E' and resid 243 through 245 removed outlier: 3.884A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1140 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: 2.43 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: 1.23 - 1.35: 2724 1.35 - 1.47: 2151 1.47 - 1.58: 3748 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 8713 Sorted by residual: bond pdb=" NZ HVU R 501 " pdb=" CA1 HVU R 501 " ideal model delta sigma weight residual 1.454 1.318 0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" NZ HVU R 501 " pdb=" CJ HVU R 501 " ideal model delta sigma weight residual 1.441 1.310 0.131 2.00e-02 2.50e+03 4.32e+01 bond pdb=" NZ HVU R 501 " pdb=" CF1 HVU R 501 " ideal model delta sigma weight residual 1.449 1.342 0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" CD1 HVU R 501 " pdb=" NE1 HVU R 501 " ideal model delta sigma weight residual 1.364 1.282 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" CD2 HVU R 501 " pdb=" CE2 HVU R 501 " ideal model delta sigma weight residual 1.412 1.489 -0.077 2.00e-02 2.50e+03 1.50e+01 ... (remaining 8708 not shown) Histogram of bond angle deviations from ideal: 98.91 - 107.01: 192 107.01 - 115.11: 5338 115.11 - 123.21: 5805 123.21 - 131.31: 442 131.31 - 139.40: 24 Bond angle restraints: 11801 Sorted by residual: angle pdb=" CD1 HVU R 501 " pdb=" NE1 HVU R 501 " pdb=" CE2 HVU R 501 " ideal model delta sigma weight residual 108.93 120.77 -11.84 3.00e+00 1.11e-01 1.56e+01 angle pdb=" N ARG E 67 " pdb=" CA ARG E 67 " pdb=" C ARG E 67 " ideal model delta sigma weight residual 114.04 110.75 3.29 1.24e+00 6.50e-01 7.05e+00 angle pdb=" CG HVU R 501 " pdb=" CD1 HVU R 501 " pdb=" NE1 HVU R 501 " ideal model delta sigma weight residual 110.60 104.25 6.35 3.00e+00 1.11e-01 4.48e+00 angle pdb=" NE1 HVU R 501 " pdb=" CE2 HVU R 501 " pdb=" CZ2 HVU R 501 " ideal model delta sigma weight residual 130.54 136.63 -6.09 3.00e+00 1.11e-01 4.12e+00 angle pdb=" CD2 HVU R 501 " pdb=" CE2 HVU R 501 " pdb=" NE1 HVU R 501 " ideal model delta sigma weight residual 107.63 101.78 5.85 3.00e+00 1.11e-01 3.81e+00 ... (remaining 11796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.44: 5004 26.44 - 52.89: 164 52.89 - 79.33: 10 79.33 - 105.78: 4 105.78 - 132.22: 1 Dihedral angle restraints: 5183 sinusoidal: 2026 harmonic: 3157 Sorted by residual: dihedral pdb=" CB1 HVU R 501 " pdb=" NZ HVU R 501 " pdb=" CF1 HVU R 501 " pdb=" CA1 HVU R 501 " ideal model delta sinusoidal sigma weight residual -69.87 62.35 -132.22 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" CA HVU R 501 " pdb=" NZ HVU R 501 " pdb=" CA1 HVU R 501 " pdb=" CF1 HVU R 501 " ideal model delta sinusoidal sigma weight residual 39.14 -59.98 99.12 1 3.00e+01 1.11e-03 1.24e+01 dihedral pdb=" CB HVU R 501 " pdb=" CB1 HVU R 501 " pdb=" CF1 HVU R 501 " pdb=" NZ HVU R 501 " ideal model delta sinusoidal sigma weight residual -29.70 60.47 -90.17 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 5180 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1165 0.051 - 0.101: 137 0.101 - 0.152: 51 0.152 - 0.202: 0 0.202 - 0.253: 1 Chirality restraints: 1354 Sorted by residual: chirality pdb=" CB HVU R 501 " pdb=" CA HVU R 501 " pdb=" CB1 HVU R 501 " pdb=" CG HVU R 501 " both_signs ideal model delta sigma weight residual False -2.48 -2.74 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA ILE B 81 " pdb=" N ILE B 81 " pdb=" C ILE B 81 " pdb=" CB ILE B 81 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA VAL G 54 " pdb=" N VAL G 54 " pdb=" C VAL G 54 " pdb=" CB VAL G 54 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 1351 not shown) Planarity restraints: 1470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO B 236 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 340 " 0.015 5.00e-02 4.00e+02 2.33e-02 8.68e-01 pdb=" N PRO R 341 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO R 341 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO R 341 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET E 192 " 0.004 2.00e-02 2.50e+03 7.04e-03 4.96e-01 pdb=" C MET E 192 " -0.012 2.00e-02 2.50e+03 pdb=" O MET E 192 " 0.005 2.00e-02 2.50e+03 pdb=" N SER E 193 " 0.004 2.00e-02 2.50e+03 ... (remaining 1467 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 61 2.51 - 3.11: 6558 3.11 - 3.71: 13553 3.71 - 4.30: 19411 4.30 - 4.90: 32860 Nonbonded interactions: 72443 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 1.918 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD2 ASP B 247 " model vdw 2.035 2.440 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.043 2.440 nonbonded pdb=" O ALA A 203 " pdb=" NH1 ARG A 205 " model vdw 2.130 2.520 nonbonded pdb=" O PRO R 341 " pdb=" OG1 THR R 345 " model vdw 2.153 2.440 ... (remaining 72438 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.930 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 26.490 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 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 0.136 8713 Z= 0.261 Angle : 0.449 11.836 11801 Z= 0.239 Chirality : 0.038 0.253 1354 Planarity : 0.002 0.033 1470 Dihedral : 12.839 132.220 3133 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.41 (0.27), residues: 1066 helix: 2.93 (0.27), residues: 379 sheet: 1.23 (0.31), residues: 269 loop : 0.69 (0.33), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 331 HIS 0.002 0.000 HIS G 44 PHE 0.008 0.001 PHE R 152 TYR 0.008 0.001 TYR R 192 ARG 0.004 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.916 Fit side-chains REVERT: A 243 MET cc_start: 0.8133 (tpp) cc_final: 0.7689 (tpt) REVERT: B 188 MET cc_start: 0.7847 (mmm) cc_final: 0.7638 (mmm) REVERT: B 221 THR cc_start: 0.7828 (m) cc_final: 0.7606 (m) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 1.0889 time to fit residues: 205.0508 Evaluate side-chains 134 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 295 ASN E 77 ASN E 186 GLN R 112 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 8713 Z= 0.280 Angle : 0.555 7.445 11801 Z= 0.295 Chirality : 0.043 0.140 1354 Planarity : 0.004 0.052 1470 Dihedral : 6.579 113.238 1185 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.39 % Allowed : 11.87 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.26), residues: 1066 helix: 2.31 (0.26), residues: 380 sheet: 1.03 (0.30), residues: 280 loop : 0.64 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 99 HIS 0.006 0.001 HIS B 62 PHE 0.024 0.002 PHE E 212 TYR 0.010 0.001 TYR R 192 ARG 0.006 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 152 time to evaluate : 0.974 Fit side-chains REVERT: A 216 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7619 (mt-10) REVERT: B 221 THR cc_start: 0.8138 (m) cc_final: 0.7838 (m) REVERT: E 140 MET cc_start: 0.8753 (mmm) cc_final: 0.7936 (mmt) outliers start: 13 outliers final: 7 residues processed: 155 average time/residue: 1.0265 time to fit residues: 171.7551 Evaluate side-chains 135 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 187 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** A 269 ASN E 82 GLN E 113 GLN E 179 GLN E 186 GLN R 40 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8713 Z= 0.181 Angle : 0.492 7.287 11801 Z= 0.263 Chirality : 0.040 0.136 1354 Planarity : 0.003 0.046 1470 Dihedral : 6.564 116.624 1185 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.71 % Allowed : 14.87 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.26), residues: 1066 helix: 2.17 (0.27), residues: 379 sheet: 0.81 (0.30), residues: 279 loop : 0.54 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS E 35 PHE 0.018 0.001 PHE E 212 TYR 0.010 0.001 TYR E 190 ARG 0.007 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 0.965 Fit side-chains REVERT: A 248 LYS cc_start: 0.8069 (mmtm) cc_final: 0.7807 (mmtm) REVERT: B 175 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.7130 (mp10) REVERT: E 43 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7732 (mmtm) REVERT: E 140 MET cc_start: 0.8760 (mmm) cc_final: 0.7916 (mmt) REVERT: E 166 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8412 (tt) REVERT: R 27 MET cc_start: 0.6543 (OUTLIER) cc_final: 0.6240 (mpp) outliers start: 16 outliers final: 4 residues processed: 151 average time/residue: 1.0900 time to fit residues: 176.5001 Evaluate side-chains 136 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 27 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 20.0000 chunk 72 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 259 GLN E 82 GLN E 186 GLN R 40 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8713 Z= 0.292 Angle : 0.561 8.620 11801 Z= 0.298 Chirality : 0.043 0.153 1354 Planarity : 0.003 0.033 1470 Dihedral : 6.906 117.283 1185 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.99 % Allowed : 15.51 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.26), residues: 1066 helix: 1.89 (0.26), residues: 378 sheet: 0.45 (0.30), residues: 285 loop : 0.50 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 99 HIS 0.007 0.001 HIS B 62 PHE 0.015 0.002 PHE E 212 TYR 0.011 0.001 TYR E 103 ARG 0.006 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 0.908 Fit side-chains REVERT: A 216 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7771 (mt-10) REVERT: A 309 ASP cc_start: 0.7346 (m-30) cc_final: 0.7019 (m-30) REVERT: A 327 THR cc_start: 0.6400 (OUTLIER) cc_final: 0.6102 (t) REVERT: B 43 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8690 (mp) REVERT: B 52 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7617 (mtp85) REVERT: B 134 ARG cc_start: 0.7463 (ptp-110) cc_final: 0.7193 (ptp-110) REVERT: B 175 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7317 (mp10) REVERT: B 217 MET cc_start: 0.7107 (mtp) cc_final: 0.6813 (mmp) REVERT: E 43 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7808 (mmtm) REVERT: R 27 MET cc_start: 0.6551 (OUTLIER) cc_final: 0.6244 (mpp) outliers start: 28 outliers final: 7 residues processed: 147 average time/residue: 1.1494 time to fit residues: 180.5601 Evaluate side-chains 136 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 27 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 0 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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** A 269 ASN B 259 GLN E 82 GLN E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 8713 Z= 0.389 Angle : 0.601 8.294 11801 Z= 0.321 Chirality : 0.045 0.142 1354 Planarity : 0.004 0.034 1470 Dihedral : 7.276 119.046 1185 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.64 % Allowed : 16.79 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.26), residues: 1066 helix: 1.52 (0.27), residues: 381 sheet: 0.26 (0.30), residues: 290 loop : 0.42 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 99 HIS 0.008 0.001 HIS R 112 PHE 0.012 0.002 PHE A 334 TYR 0.018 0.002 TYR E 103 ARG 0.010 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 128 time to evaluate : 0.967 Fit side-chains REVERT: A 216 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7793 (mt-10) REVERT: A 309 ASP cc_start: 0.7358 (m-30) cc_final: 0.7063 (m-30) REVERT: A 327 THR cc_start: 0.6304 (OUTLIER) cc_final: 0.6082 (t) REVERT: B 175 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7240 (mp10) REVERT: B 217 MET cc_start: 0.7171 (mtp) cc_final: 0.6898 (mmp) REVERT: E 18 ARG cc_start: 0.8213 (tpp80) cc_final: 0.8004 (ttm-80) REVERT: E 43 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8040 (mmtm) REVERT: E 166 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8473 (tt) REVERT: R 27 MET cc_start: 0.6596 (OUTLIER) cc_final: 0.6300 (mpp) outliers start: 34 outliers final: 17 residues processed: 147 average time/residue: 1.1044 time to fit residues: 173.6871 Evaluate side-chains 144 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 27 MET Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 330 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** A 269 ASN B 259 GLN E 82 GLN E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8713 Z= 0.208 Angle : 0.528 8.640 11801 Z= 0.278 Chirality : 0.041 0.142 1354 Planarity : 0.003 0.033 1470 Dihedral : 6.903 117.824 1185 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.21 % Allowed : 18.40 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.26), residues: 1066 helix: 1.68 (0.27), residues: 381 sheet: 0.26 (0.30), residues: 282 loop : 0.45 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS R 112 PHE 0.010 0.001 PHE A 334 TYR 0.013 0.001 TYR E 103 ARG 0.007 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 129 time to evaluate : 0.993 Fit side-chains REVERT: A 248 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7663 (mmtm) REVERT: A 263 SER cc_start: 0.8019 (m) cc_final: 0.7745 (t) REVERT: A 309 ASP cc_start: 0.7282 (m-30) cc_final: 0.7015 (m-30) REVERT: A 318 GLU cc_start: 0.6982 (tp30) cc_final: 0.6599 (tp30) REVERT: B 43 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8514 (mp) REVERT: B 175 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7347 (mp10) REVERT: B 217 MET cc_start: 0.7177 (mtp) cc_final: 0.6854 (mmp) REVERT: B 234 PHE cc_start: 0.9312 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: E 43 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7948 (mmtm) REVERT: R 27 MET cc_start: 0.6524 (OUTLIER) cc_final: 0.6278 (mpp) REVERT: R 82 TYR cc_start: 0.8643 (t80) cc_final: 0.8319 (t80) outliers start: 30 outliers final: 14 residues processed: 144 average time/residue: 1.1185 time to fit residues: 172.9516 Evaluate side-chains 146 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 27 MET Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 198 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 62 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 61 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 259 GLN E 82 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8713 Z= 0.179 Angle : 0.522 9.065 11801 Z= 0.273 Chirality : 0.041 0.183 1354 Planarity : 0.003 0.033 1470 Dihedral : 6.751 117.289 1185 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.67 % Allowed : 19.04 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.26), residues: 1066 helix: 1.72 (0.27), residues: 382 sheet: 0.32 (0.30), residues: 279 loop : 0.47 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS R 112 PHE 0.010 0.001 PHE A 334 TYR 0.018 0.001 TYR E 59 ARG 0.007 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 1.018 Fit side-chains REVERT: A 243 MET cc_start: 0.8106 (mmm) cc_final: 0.7869 (tpt) REVERT: A 263 SER cc_start: 0.8072 (m) cc_final: 0.7783 (t) REVERT: A 309 ASP cc_start: 0.7240 (m-30) cc_final: 0.6981 (m-30) REVERT: A 318 GLU cc_start: 0.6947 (tp30) cc_final: 0.6583 (tp30) REVERT: B 175 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7317 (mp10) REVERT: B 217 MET cc_start: 0.7001 (mtp) cc_final: 0.6773 (mmp) REVERT: B 219 ARG cc_start: 0.7776 (mpt180) cc_final: 0.7424 (mpt180) REVERT: B 234 PHE cc_start: 0.9322 (OUTLIER) cc_final: 0.7917 (m-80) outliers start: 25 outliers final: 13 residues processed: 141 average time/residue: 1.2164 time to fit residues: 183.8880 Evaluate side-chains 144 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 338 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.0050 chunk 64 optimal weight: 0.0970 chunk 69 optimal weight: 0.9980 chunk 50 optimal weight: 0.0020 chunk 9 optimal weight: 1.9990 chunk 80 optimal weight: 0.1980 chunk 92 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 overall best weight: 0.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 259 GLN E 82 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 8713 Z= 0.147 Angle : 0.516 9.819 11801 Z= 0.267 Chirality : 0.040 0.165 1354 Planarity : 0.003 0.034 1470 Dihedral : 6.618 118.027 1185 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.03 % Allowed : 20.53 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1066 helix: 1.83 (0.27), residues: 380 sheet: 0.27 (0.30), residues: 274 loop : 0.44 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 331 HIS 0.003 0.001 HIS A 195 PHE 0.008 0.001 PHE A 334 TYR 0.011 0.001 TYR R 182 ARG 0.008 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 1.042 Fit side-chains REVERT: A 243 MET cc_start: 0.8135 (mmm) cc_final: 0.7874 (tpt) REVERT: A 309 ASP cc_start: 0.7201 (m-30) cc_final: 0.6924 (m-30) REVERT: B 175 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.7166 (mp10) REVERT: B 217 MET cc_start: 0.7042 (mtp) cc_final: 0.6760 (mmp) REVERT: B 219 ARG cc_start: 0.7728 (mpt180) cc_final: 0.7493 (mpt180) outliers start: 19 outliers final: 10 residues processed: 150 average time/residue: 1.1991 time to fit residues: 191.9612 Evaluate side-chains 142 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 338 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 10.0000 chunk 97 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 29 optimal weight: 0.3980 chunk 86 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 259 GLN E 82 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8713 Z= 0.194 Angle : 0.540 10.454 11801 Z= 0.278 Chirality : 0.041 0.166 1354 Planarity : 0.004 0.061 1470 Dihedral : 6.661 117.176 1185 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.03 % Allowed : 20.53 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.26), residues: 1066 helix: 1.80 (0.27), residues: 379 sheet: 0.30 (0.30), residues: 280 loop : 0.52 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 331 HIS 0.003 0.001 HIS R 112 PHE 0.021 0.001 PHE A 334 TYR 0.021 0.001 TYR E 59 ARG 0.011 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.001 Fit side-chains REVERT: A 24 ARG cc_start: 0.7108 (mtm-85) cc_final: 0.6746 (ttm110) REVERT: A 243 MET cc_start: 0.8134 (mmm) cc_final: 0.7884 (tpt) REVERT: A 309 ASP cc_start: 0.7234 (m-30) cc_final: 0.6954 (m-30) REVERT: B 175 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.7184 (mp10) REVERT: B 217 MET cc_start: 0.7064 (mtp) cc_final: 0.6767 (mmp) REVERT: B 219 ARG cc_start: 0.7750 (mpt180) cc_final: 0.7498 (mpt180) REVERT: B 234 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: E 43 LYS cc_start: 0.8073 (mtmm) cc_final: 0.7854 (mmtm) outliers start: 19 outliers final: 14 residues processed: 141 average time/residue: 1.1777 time to fit residues: 177.3936 Evaluate side-chains 146 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 89 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 259 GLN E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8713 Z= 0.189 Angle : 0.542 11.025 11801 Z= 0.280 Chirality : 0.041 0.180 1354 Planarity : 0.004 0.063 1470 Dihedral : 6.731 118.490 1185 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.93 % Allowed : 21.39 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1066 helix: 1.78 (0.27), residues: 380 sheet: 0.29 (0.30), residues: 270 loop : 0.49 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 331 HIS 0.003 0.001 HIS R 112 PHE 0.010 0.001 PHE E 68 TYR 0.010 0.001 TYR E 103 ARG 0.015 0.001 ARG E 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 1.012 Fit side-chains REVERT: A 243 MET cc_start: 0.8134 (mmm) cc_final: 0.7878 (tpt) REVERT: A 309 ASP cc_start: 0.7237 (m-30) cc_final: 0.6955 (m-30) REVERT: B 175 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.7173 (mp10) REVERT: B 217 MET cc_start: 0.7125 (mtp) cc_final: 0.6812 (mmp) REVERT: B 219 ARG cc_start: 0.7743 (mpt180) cc_final: 0.7433 (mpt180) REVERT: B 234 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.7893 (m-80) REVERT: E 43 LYS cc_start: 0.8064 (mtmm) cc_final: 0.7820 (mmtm) REVERT: G 21 MET cc_start: 0.7941 (tmt) cc_final: 0.7480 (tmt) outliers start: 18 outliers final: 12 residues processed: 138 average time/residue: 1.1316 time to fit residues: 167.1867 Evaluate side-chains 142 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 12 optimal weight: 0.1980 chunk 23 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 86 optimal weight: 0.0570 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 259 GLN E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.175337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.139847 restraints weight = 9690.259| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.14 r_work: 0.3459 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8713 Z= 0.170 Angle : 0.537 10.637 11801 Z= 0.276 Chirality : 0.041 0.170 1354 Planarity : 0.004 0.059 1470 Dihedral : 6.626 117.485 1185 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.93 % Allowed : 21.07 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.26), residues: 1066 helix: 1.75 (0.27), residues: 379 sheet: 0.23 (0.31), residues: 266 loop : 0.48 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 331 HIS 0.003 0.001 HIS A 195 PHE 0.009 0.001 PHE E 68 TYR 0.025 0.001 TYR E 59 ARG 0.015 0.001 ARG E 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3584.35 seconds wall clock time: 64 minutes 41.31 seconds (3881.31 seconds total)