Starting phenix.real_space_refine on Mon Mar 11 18:00:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmv_30411/03_2024/7cmv_30411_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmv_30411/03_2024/7cmv_30411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmv_30411/03_2024/7cmv_30411.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmv_30411/03_2024/7cmv_30411.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmv_30411/03_2024/7cmv_30411_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmv_30411/03_2024/7cmv_30411_neut_updated.pdb" } resolution = 2.7 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= 0.009 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 67 5.16 5 C 5575 2.51 5 N 1489 2.21 5 O 1644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E ARG 160": "NH1" <-> "NH2" Residue "E GLU 246": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8775 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1813 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 2 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "C" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 447 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Chain: "R" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2146 Unusual residues: {'G6O': 1} Inner-chain residues flagged as termini: ['pdbres="CYS R 400 "'] Classifications: {'peptide': 272, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 261, None: 1} Not linked: pdbres="CYS R 400 " pdbres="G6O R 500 " Chain breaks: 1 Time building chain proxies: 5.41, per 1000 atoms: 0.62 Number of scatterers: 8775 At special positions: 0 Unit cell: (104.442, 129.792, 114.582, 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 67 16.00 O 1644 8.00 N 1489 7.00 C 5575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 103 " - pdb=" SG CYS R 181 " distance=2.03 Simple disulfide: pdb=" SG CYS R 355 " - pdb=" SG CYS R 358 " 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: 3.55 Conformation dependent library (CDL) restraints added in 1.7 seconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 12 sheets defined 36.7% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.816A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 46 through 56 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 227 through 231 removed outlier: 4.118A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 231' 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 278 removed outlier: 3.832A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (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 removed outlier: 3.795A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 removed outlier: 4.018A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.540A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.586A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 30 through 43 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 'R' and resid 33 through 56 Processing helix chain 'R' and resid 63 through 81 removed outlier: 4.109A pdb=" N LEU R 67 " --> pdb=" O THR R 63 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL R 68 " --> pdb=" O THR R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 92 Processing helix chain 'R' and resid 100 through 133 Processing helix chain 'R' and resid 135 through 141 removed outlier: 6.387A pdb=" N HIS R 140 " --> pdb=" O VAL R 136 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLY R 141 " --> pdb=" O HIS R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 169 removed outlier: 3.557A pdb=" N ARG R 149 " --> pdb=" O SER R 145 " (cutoff:3.500A) Proline residue: R 167 - end of helix Processing helix chain 'R' and resid 186 through 222 removed outlier: 3.917A pdb=" N ILE R 190 " --> pdb=" O PRO R 186 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TYR R 191 " --> pdb=" O ASP R 187 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU R 199 " --> pdb=" O VAL R 195 " (cutoff:3.500A) Proline residue: R 200 - end of helix Processing helix chain 'R' and resid 322 through 354 Proline residue: R 344 - end of helix Processing helix chain 'R' and resid 362 through 384 removed outlier: 3.691A pdb=" N ASN R 375 " --> pdb=" O LEU R 371 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER R 376 " --> pdb=" O GLY R 372 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA R 377 " --> pdb=" O TYR R 373 " (cutoff:3.500A) Proline residue: R 380 - end of helix Processing helix chain 'R' and resid 388 through 399 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.679A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N GLY A 40 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.716A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.215A 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: 6.675A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.123A 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: 6.572A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.929A 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: 6.875A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.370A 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: 6.400A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 5.799A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.308A 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: 6.781A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 13 removed outlier: 4.030A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.973A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 155 through 160 removed outlier: 3.501A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1176 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: 2.91 Time building geometry restraints manager: 3.83 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: 1470 1.32 - 1.44: 2418 1.44 - 1.57: 4969 1.57 - 1.69: 3 1.69 - 1.81: 95 Bond restraints: 8955 Sorted by residual: bond pdb=" C2 G6O R 500 " pdb=" C4 G6O R 500 " ideal model delta sigma weight residual 1.392 1.614 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C1 G6O R 500 " pdb=" C3 G6O R 500 " ideal model delta sigma weight residual 1.392 1.593 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C5 G6O R 500 " pdb=" C6 G6O R 500 " ideal model delta sigma weight residual 1.393 1.200 0.193 2.00e-02 2.50e+03 9.36e+01 bond pdb=" C10 G6O R 500 " pdb=" O2 G6O R 500 " ideal model delta sigma weight residual 1.426 1.259 0.167 2.00e-02 2.50e+03 6.98e+01 bond pdb=" C2 G6O R 500 " pdb=" O1 G6O R 500 " ideal model delta sigma weight residual 1.357 1.231 0.126 2.00e-02 2.50e+03 3.98e+01 ... (remaining 8950 not shown) Histogram of bond angle deviations from ideal: 99.79 - 106.63: 194 106.63 - 113.47: 4949 113.47 - 120.31: 3109 120.31 - 127.15: 3796 127.15 - 133.99: 91 Bond angle restraints: 12139 Sorted by residual: angle pdb=" C10 G6O R 500 " pdb=" O2 G6O R 500 " pdb=" C7 G6O R 500 " ideal model delta sigma weight residual 113.23 129.59 -16.36 3.00e+00 1.11e-01 2.97e+01 angle pdb=" C2 G6O R 500 " pdb=" O1 G6O R 500 " pdb=" C8 G6O R 500 " ideal model delta sigma weight residual 117.80 130.12 -12.32 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C4 G6O R 500 " pdb=" C2 G6O R 500 " pdb=" O1 G6O R 500 " ideal model delta sigma weight residual 117.00 126.76 -9.76 3.00e+00 1.11e-01 1.06e+01 angle pdb=" N HIS R 349 " pdb=" CA HIS R 349 " pdb=" C HIS R 349 " ideal model delta sigma weight residual 111.07 107.80 3.27 1.07e+00 8.73e-01 9.33e+00 angle pdb=" C THR R 348 " pdb=" N HIS R 349 " pdb=" CA HIS R 349 " ideal model delta sigma weight residual 120.44 124.03 -3.59 1.30e+00 5.92e-01 7.64e+00 ... (remaining 12134 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4967 17.93 - 35.86: 300 35.86 - 53.79: 39 53.79 - 71.72: 15 71.72 - 89.64: 10 Dihedral angle restraints: 5331 sinusoidal: 2071 harmonic: 3260 Sorted by residual: dihedral pdb=" CB CYS E 159 " pdb=" SG CYS E 159 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual 93.00 61.37 31.63 1 1.00e+01 1.00e-02 1.43e+01 dihedral pdb=" CA LEU A 268 " pdb=" C LEU A 268 " pdb=" N ASN A 269 " pdb=" CA ASN A 269 " ideal model delta harmonic sigma weight residual 180.00 -163.41 -16.59 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CB GLU B 10 " pdb=" CG GLU B 10 " pdb=" CD GLU B 10 " pdb=" OE1 GLU B 10 " ideal model delta sinusoidal sigma weight residual 0.00 89.64 -89.64 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 5328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 869 0.027 - 0.053: 327 0.053 - 0.080: 99 0.080 - 0.107: 57 0.107 - 0.134: 41 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA VAL E 2 " pdb=" N VAL E 2 " pdb=" C VAL E 2 " pdb=" CB VAL E 2 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA ILE E 216 " pdb=" N ILE E 216 " pdb=" C ILE E 216 " pdb=" CB ILE E 216 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 1390 not shown) Planarity restraints: 1528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 74 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.01e+00 pdb=" N PRO E 75 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO E 75 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 75 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS R 349 " 0.007 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C HIS R 349 " -0.027 2.00e-02 2.50e+03 pdb=" O HIS R 349 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL R 350 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 13 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.09e+00 pdb=" C ARG C 13 " -0.025 2.00e-02 2.50e+03 pdb=" O ARG C 13 " 0.009 2.00e-02 2.50e+03 pdb=" N LYS C 14 " 0.008 2.00e-02 2.50e+03 ... (remaining 1525 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 102 2.61 - 3.18: 7621 3.18 - 3.75: 13255 3.75 - 4.33: 18822 4.33 - 4.90: 32099 Nonbonded interactions: 71899 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.032 2.440 nonbonded pdb=" OG1 THR E 150 " pdb=" OE1 GLU E 153 " model vdw 2.091 2.440 nonbonded pdb=" O PHE E 29 " pdb=" NH2 ARG E 72 " model vdw 2.161 2.520 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.162 2.520 nonbonded pdb=" OD1 ASP A 315 " pdb=" N THR A 316 " model vdw 2.207 2.520 ... (remaining 71894 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.170 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 28.040 Find NCS groups from input model: 0.260 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:10.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 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 : 0.005 0.222 8955 Z= 0.410 Angle : 0.487 16.359 12139 Z= 0.260 Chirality : 0.039 0.134 1393 Planarity : 0.002 0.056 1528 Dihedral : 12.439 89.644 3218 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 2.95 (0.26), residues: 1105 helix: 3.91 (0.25), residues: 374 sheet: 1.44 (0.31), residues: 269 loop : 0.65 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 85 HIS 0.002 0.000 HIS A 188 PHE 0.009 0.001 PHE R 345 TYR 0.004 0.000 TYR R 212 ARG 0.007 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.046 Fit side-chains REVERT: B 19 ARG cc_start: 0.7451 (ttt-90) cc_final: 0.6718 (ttm110) REVERT: B 47 THR cc_start: 0.8744 (t) cc_final: 0.8494 (m) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 1.2620 time to fit residues: 237.9541 Evaluate side-chains 131 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS B 75 GLN B 175 GLN E 39 GLN E 179 GLN E 194 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8955 Z= 0.289 Angle : 0.600 9.944 12139 Z= 0.315 Chirality : 0.045 0.176 1393 Planarity : 0.004 0.050 1528 Dihedral : 4.190 22.767 1239 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.33 % Allowed : 8.32 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 2.37 (0.25), residues: 1105 helix: 3.37 (0.25), residues: 379 sheet: 1.17 (0.30), residues: 280 loop : 0.28 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 99 HIS 0.008 0.001 HIS R 349 PHE 0.017 0.002 PHE R 345 TYR 0.012 0.001 TYR R 383 ARG 0.009 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 1.164 Fit side-chains REVERT: B 19 ARG cc_start: 0.7531 (ttt-90) cc_final: 0.6765 (ttm110) REVERT: B 22 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.5973 (mtt180) REVERT: B 258 ASP cc_start: 0.8059 (t0) cc_final: 0.6982 (t0) REVERT: E 113 GLN cc_start: 0.7905 (mm110) cc_final: 0.7622 (mm110) REVERT: R 212 TYR cc_start: 0.7247 (t80) cc_final: 0.6990 (t80) outliers start: 32 outliers final: 10 residues processed: 154 average time/residue: 1.2944 time to fit residues: 211.7451 Evaluate side-chains 135 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 335 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 7.9990 chunk 31 optimal weight: 0.4980 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN E 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8955 Z= 0.133 Angle : 0.471 8.131 12139 Z= 0.249 Chirality : 0.040 0.150 1393 Planarity : 0.003 0.043 1528 Dihedral : 3.865 19.901 1239 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.60 % Allowed : 11.64 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 2.34 (0.25), residues: 1105 helix: 3.57 (0.25), residues: 379 sheet: 1.20 (0.30), residues: 272 loop : 0.00 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.004 0.001 HIS R 349 PHE 0.013 0.001 PHE R 345 TYR 0.007 0.001 TYR B 124 ARG 0.012 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 273 LEU cc_start: 0.7791 (tt) cc_final: 0.7244 (mp) REVERT: A 318 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7048 (tt0) REVERT: B 19 ARG cc_start: 0.7521 (ttt-90) cc_final: 0.6765 (ttm110) REVERT: B 303 ASP cc_start: 0.7719 (m-30) cc_final: 0.7491 (m-30) REVERT: E 113 GLN cc_start: 0.7788 (mm110) cc_final: 0.7505 (mm110) outliers start: 25 outliers final: 12 residues processed: 145 average time/residue: 1.2777 time to fit residues: 197.1490 Evaluate side-chains 138 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 364 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 10.0000 chunk 75 optimal weight: 0.0170 chunk 51 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 175 GLN E 142 GLN E 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8955 Z= 0.221 Angle : 0.539 9.375 12139 Z= 0.281 Chirality : 0.042 0.153 1393 Planarity : 0.004 0.042 1528 Dihedral : 4.201 22.502 1239 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.95 % Allowed : 11.54 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 2.00 (0.25), residues: 1105 helix: 3.28 (0.25), residues: 381 sheet: 0.90 (0.30), residues: 280 loop : -0.13 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS R 349 PHE 0.015 0.001 PHE R 345 TYR 0.012 0.001 TYR E 59 ARG 0.013 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 125 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.7067 (m-30) REVERT: A 273 LEU cc_start: 0.7734 (tt) cc_final: 0.7279 (mp) REVERT: B 19 ARG cc_start: 0.7558 (ttt-90) cc_final: 0.6800 (ttp80) REVERT: B 22 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6141 (mtt180) REVERT: B 214 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.6833 (mpt-90) REVERT: B 258 ASP cc_start: 0.8277 (t0) cc_final: 0.7212 (t0) REVERT: B 303 ASP cc_start: 0.7753 (m-30) cc_final: 0.7528 (m-30) REVERT: B 322 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8213 (m-30) REVERT: E 113 GLN cc_start: 0.7837 (mm110) cc_final: 0.7587 (mm110) REVERT: R 58 ARG cc_start: 0.7126 (tmt-80) cc_final: 0.5700 (mmt180) REVERT: R 139 GLN cc_start: 0.6567 (OUTLIER) cc_final: 0.5710 (tt0) outliers start: 38 outliers final: 16 residues processed: 145 average time/residue: 1.2254 time to fit residues: 189.0895 Evaluate side-chains 143 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 139 GLN Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 364 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN E 39 GLN E 142 GLN E 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8955 Z= 0.288 Angle : 0.579 9.648 12139 Z= 0.302 Chirality : 0.044 0.176 1393 Planarity : 0.004 0.042 1528 Dihedral : 4.466 25.190 1239 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.68 % Allowed : 11.64 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 1.70 (0.25), residues: 1105 helix: 3.01 (0.26), residues: 379 sheet: 0.73 (0.29), residues: 282 loop : -0.27 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 169 HIS 0.005 0.001 HIS R 349 PHE 0.017 0.002 PHE R 345 TYR 0.009 0.001 TYR B 85 ARG 0.013 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 121 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.7076 (m-30) REVERT: A 273 LEU cc_start: 0.7840 (tt) cc_final: 0.7317 (mp) REVERT: B 19 ARG cc_start: 0.7396 (ttt-90) cc_final: 0.6696 (ttp80) REVERT: B 22 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6128 (mtt180) REVERT: B 214 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6835 (mpt-90) REVERT: B 258 ASP cc_start: 0.8334 (t0) cc_final: 0.7281 (t0) REVERT: B 303 ASP cc_start: 0.7775 (m-30) cc_final: 0.7549 (m-30) REVERT: B 322 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8246 (m-30) REVERT: E 43 LYS cc_start: 0.8165 (mppt) cc_final: 0.7962 (mppt) REVERT: E 89 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7314 (pm20) REVERT: E 113 GLN cc_start: 0.7908 (mm110) cc_final: 0.7601 (mm110) REVERT: R 58 ARG cc_start: 0.7141 (tmt-80) cc_final: 0.5769 (mmt180) REVERT: R 139 GLN cc_start: 0.6739 (OUTLIER) cc_final: 0.5900 (tt0) REVERT: R 330 MET cc_start: 0.8138 (tpp) cc_final: 0.7923 (tpp) outliers start: 45 outliers final: 19 residues processed: 147 average time/residue: 1.2270 time to fit residues: 192.2213 Evaluate side-chains 146 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 139 GLN Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 364 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 0.1980 chunk 102 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 239 ASN E 142 GLN E 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8955 Z= 0.144 Angle : 0.483 7.932 12139 Z= 0.253 Chirality : 0.041 0.156 1393 Planarity : 0.003 0.062 1528 Dihedral : 4.014 21.212 1239 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.43 % Allowed : 13.41 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 1.84 (0.25), residues: 1105 helix: 3.32 (0.26), residues: 376 sheet: 0.79 (0.30), residues: 272 loop : -0.33 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS R 349 PHE 0.014 0.001 PHE R 345 TYR 0.005 0.001 TYR B 124 ARG 0.015 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 130 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: A 273 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7333 (mp) REVERT: B 19 ARG cc_start: 0.7383 (ttt-90) cc_final: 0.6679 (ttp80) REVERT: B 22 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.6025 (mtt180) REVERT: B 156 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8467 (pt0) REVERT: B 258 ASP cc_start: 0.8206 (t0) cc_final: 0.7240 (t0) REVERT: B 262 MET cc_start: 0.8131 (ttm) cc_final: 0.7852 (ttm) REVERT: E 43 LYS cc_start: 0.8143 (mppt) cc_final: 0.7891 (mppt) REVERT: E 113 GLN cc_start: 0.7836 (mm110) cc_final: 0.7530 (mm110) REVERT: R 58 ARG cc_start: 0.7068 (tmt-80) cc_final: 0.5690 (mmt180) REVERT: R 139 GLN cc_start: 0.6493 (OUTLIER) cc_final: 0.5626 (tt0) outliers start: 33 outliers final: 15 residues processed: 149 average time/residue: 1.2272 time to fit residues: 195.3687 Evaluate side-chains 145 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 139 GLN Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 347 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 59 optimal weight: 0.0970 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 0.0020 chunk 64 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 175 GLN E 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8955 Z= 0.167 Angle : 0.500 8.291 12139 Z= 0.260 Chirality : 0.041 0.139 1393 Planarity : 0.004 0.066 1528 Dihedral : 4.007 20.936 1239 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.53 % Allowed : 13.31 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 1.83 (0.25), residues: 1105 helix: 3.31 (0.26), residues: 376 sheet: 0.90 (0.31), residues: 268 loop : -0.40 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS R 349 PHE 0.014 0.001 PHE R 345 TYR 0.006 0.001 TYR E 103 ARG 0.017 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 128 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: A 273 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7338 (mp) REVERT: B 19 ARG cc_start: 0.7385 (ttt-90) cc_final: 0.6677 (ttp80) REVERT: B 22 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.6033 (mtt180) REVERT: B 118 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7501 (p0) REVERT: B 258 ASP cc_start: 0.8217 (t0) cc_final: 0.7230 (t0) REVERT: B 262 MET cc_start: 0.8204 (ttm) cc_final: 0.7939 (ttm) REVERT: E 18 ARG cc_start: 0.8268 (tpp-160) cc_final: 0.7986 (tpp-160) REVERT: E 43 LYS cc_start: 0.8141 (mppt) cc_final: 0.7832 (mppt) REVERT: E 113 GLN cc_start: 0.7799 (mm110) cc_final: 0.7518 (mm110) REVERT: R 58 ARG cc_start: 0.7086 (tmt-80) cc_final: 0.5730 (mmt180) REVERT: R 139 GLN cc_start: 0.6508 (OUTLIER) cc_final: 0.5630 (tt0) REVERT: R 330 MET cc_start: 0.8160 (tpp) cc_final: 0.7938 (tpp) outliers start: 34 outliers final: 19 residues processed: 147 average time/residue: 1.2267 time to fit residues: 192.4316 Evaluate side-chains 149 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 139 GLN Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 347 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 72 optimal weight: 0.0870 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** R 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 8955 Z= 0.336 Angle : 0.613 9.789 12139 Z= 0.318 Chirality : 0.045 0.194 1393 Planarity : 0.004 0.064 1528 Dihedral : 4.506 25.478 1239 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.16 % Allowed : 13.31 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 1.49 (0.25), residues: 1105 helix: 2.89 (0.26), residues: 378 sheet: 0.67 (0.30), residues: 279 loop : -0.47 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 169 HIS 0.006 0.001 HIS R 349 PHE 0.018 0.002 PHE R 345 TYR 0.012 0.002 TYR E 103 ARG 0.016 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 127 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.7160 (m-30) REVERT: A 23 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8021 (mp) REVERT: A 273 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7327 (mp) REVERT: B 19 ARG cc_start: 0.7403 (ttt-90) cc_final: 0.6687 (ttp80) REVERT: B 22 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6145 (mtt180) REVERT: B 118 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7641 (p0) REVERT: B 156 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8587 (mt0) REVERT: B 214 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.6857 (mpt-90) REVERT: B 258 ASP cc_start: 0.8318 (t0) cc_final: 0.7305 (t0) REVERT: B 267 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7549 (t0) REVERT: B 303 ASP cc_start: 0.7806 (m-30) cc_final: 0.7604 (m-30) REVERT: B 336 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8310 (mt) REVERT: E 18 ARG cc_start: 0.8279 (tpp-160) cc_final: 0.8011 (tpp-160) REVERT: E 43 LYS cc_start: 0.8151 (mppt) cc_final: 0.7805 (mppt) REVERT: E 113 GLN cc_start: 0.7908 (mm110) cc_final: 0.7646 (mm110) REVERT: R 58 ARG cc_start: 0.7132 (tmt-80) cc_final: 0.5793 (mmt180) REVERT: R 212 TYR cc_start: 0.7361 (t80) cc_final: 0.7123 (t80) outliers start: 40 outliers final: 16 residues processed: 153 average time/residue: 1.1921 time to fit residues: 194.6044 Evaluate side-chains 149 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 335 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 59 optimal weight: 0.0370 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8955 Z= 0.150 Angle : 0.498 8.023 12139 Z= 0.260 Chirality : 0.041 0.167 1393 Planarity : 0.004 0.077 1528 Dihedral : 4.036 21.358 1239 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.91 % Allowed : 14.24 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 1.70 (0.25), residues: 1105 helix: 3.22 (0.26), residues: 376 sheet: 0.82 (0.31), residues: 267 loop : -0.49 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS R 349 PHE 0.014 0.001 PHE R 345 TYR 0.010 0.001 TYR R 191 ARG 0.018 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 273 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7292 (mp) REVERT: B 19 ARG cc_start: 0.7377 (ttt-90) cc_final: 0.6669 (ttp80) REVERT: B 22 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6036 (mtt180) REVERT: B 118 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7537 (p0) REVERT: B 156 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8479 (pt0) REVERT: B 258 ASP cc_start: 0.8195 (t0) cc_final: 0.7184 (t0) REVERT: B 262 MET cc_start: 0.8158 (ttm) cc_final: 0.7852 (ttm) REVERT: B 267 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7544 (t0) REVERT: E 18 ARG cc_start: 0.8228 (tpp-160) cc_final: 0.7964 (tpp-160) REVERT: E 43 LYS cc_start: 0.8143 (mppt) cc_final: 0.7792 (mppt) REVERT: E 113 GLN cc_start: 0.7807 (mm110) cc_final: 0.7539 (mm110) REVERT: R 58 ARG cc_start: 0.7087 (tmt-80) cc_final: 0.5712 (mmt180) REVERT: R 330 MET cc_start: 0.8031 (tpp) cc_final: 0.7546 (mmt) outliers start: 28 outliers final: 17 residues processed: 146 average time/residue: 1.2540 time to fit residues: 194.8792 Evaluate side-chains 148 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 335 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 75 GLN B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8955 Z= 0.178 Angle : 0.515 8.310 12139 Z= 0.267 Chirality : 0.041 0.175 1393 Planarity : 0.004 0.079 1528 Dihedral : 4.062 21.449 1239 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.70 % Allowed : 15.18 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 1.69 (0.25), residues: 1105 helix: 3.19 (0.26), residues: 377 sheet: 0.82 (0.31), residues: 268 loop : -0.48 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS R 349 PHE 0.014 0.001 PHE R 345 TYR 0.011 0.001 TYR R 191 ARG 0.019 0.000 ARG A 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 127 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 273 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7290 (mp) REVERT: B 19 ARG cc_start: 0.7383 (ttt-90) cc_final: 0.6671 (ttp80) REVERT: B 22 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6036 (mtt180) REVERT: B 118 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7574 (p0) REVERT: B 156 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8516 (pt0) REVERT: B 258 ASP cc_start: 0.8222 (t0) cc_final: 0.7211 (t0) REVERT: B 262 MET cc_start: 0.8153 (ttm) cc_final: 0.7852 (ttm) REVERT: B 267 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7589 (t0) REVERT: E 18 ARG cc_start: 0.8236 (tpp-160) cc_final: 0.7963 (tpp-160) REVERT: E 43 LYS cc_start: 0.8178 (mppt) cc_final: 0.7819 (mppt) REVERT: R 58 ARG cc_start: 0.7060 (tmt-80) cc_final: 0.5761 (mmt180) REVERT: R 330 MET cc_start: 0.8049 (tpp) cc_final: 0.7535 (mmt) outliers start: 26 outliers final: 17 residues processed: 142 average time/residue: 1.2055 time to fit residues: 182.5643 Evaluate side-chains 148 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 335 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.3980 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 0.2980 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.166998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.119592 restraints weight = 9929.080| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.00 r_work: 0.3235 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8955 Z= 0.215 Angle : 0.537 8.711 12139 Z= 0.279 Chirality : 0.042 0.153 1393 Planarity : 0.004 0.077 1528 Dihedral : 4.195 22.638 1239 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.22 % Allowed : 14.55 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 1.61 (0.25), residues: 1105 helix: 3.08 (0.26), residues: 379 sheet: 0.79 (0.30), residues: 269 loop : -0.52 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS R 349 PHE 0.015 0.001 PHE R 345 TYR 0.010 0.001 TYR R 191 ARG 0.019 0.001 ARG A 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3845.90 seconds wall clock time: 68 minutes 58.76 seconds (4138.76 seconds total)