Starting phenix.real_space_refine on Thu Feb 15 03:52:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evz_31342/02_2024/7evz_31342_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evz_31342/02_2024/7evz_31342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evz_31342/02_2024/7evz_31342.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evz_31342/02_2024/7evz_31342.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evz_31342/02_2024/7evz_31342_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evz_31342/02_2024/7evz_31342_updated.pdb" } resolution = 3.07 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= -0.001 sd= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1983 atoms to isotropic. 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 64 5.16 5 C 5810 2.51 5 N 1521 2.21 5 O 1683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 238": "OE1" <-> "OE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 292": "NH1" <-> "NH2" Residue "E PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E GLU 246": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9078 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1838 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "D" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2296 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 6, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Unusual residues: {'JER': 1, 'PLM': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.26, per 1000 atoms: 0.58 Number of scatterers: 9078 At special positions: 0 Unit cell: (90.63, 123.975, 128.25, 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 64 16.00 O 1683 8.00 N 1521 7.00 C 5810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 191 " distance=2.03 Simple disulfide: pdb=" SG CYS D 282 " - pdb=" SG CYS D 287 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.30 Conformation dependent library (CDL) restraints added in 1.9 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 14 sheets defined 32.4% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 7 through 27 removed outlier: 3.828A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 272 through 278 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 309 removed outlier: 3.939A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 350 removed outlier: 3.646A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.695A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'D' and resid 23 through 32 Processing helix chain 'D' and resid 49 through 72 Processing helix chain 'D' and resid 79 through 104 removed outlier: 3.769A pdb=" N PHE D 83 " --> pdb=" O PRO D 79 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 84 " --> pdb=" O MET D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 111 removed outlier: 3.546A pdb=" N TYR D 110 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS D 111 " --> pdb=" O THR D 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 107 through 111' Processing helix chain 'D' and resid 114 through 147 removed outlier: 3.512A pdb=" N GLU D 121 " --> pdb=" O TRP D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 180 Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 200 through 235 removed outlier: 3.931A pdb=" N VAL D 228 " --> pdb=" O ILE D 224 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG D 234 " --> pdb=" O THR D 230 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 267 removed outlier: 3.545A pdb=" N LYS D 256 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR D 257 " --> pdb=" O ALA D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 281 removed outlier: 3.977A pdb=" N VAL D 280 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 313 removed outlier: 3.505A pdb=" N ALA D 300 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) Proline residue: D 308 - end of helix Processing helix chain 'D' and resid 316 through 324 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.861A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 199 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.087A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE B 93 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 111 through 114 removed outlier: 3.502A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.573A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.536A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.528A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 46 through 52 removed outlier: 3.544A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.530A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.512A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.780A pdb=" N THR E 118 " --> pdb=" O VAL E 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'E' and resid 115 through 117 removed outlier: 3.750A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 140 through 142 Processing sheet with id= M, first strand: chain 'E' and resid 146 through 148 removed outlier: 7.066A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 225 through 231 removed outlier: 3.553A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1080 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: 2.81 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2274 1.33 - 1.45: 1913 1.45 - 1.58: 4974 1.58 - 1.70: 3 1.70 - 1.82: 91 Bond restraints: 9255 Sorted by residual: bond pdb=" C31 JER D 401 " pdb=" C32 JER D 401 " ideal model delta sigma weight residual 1.543 1.361 0.182 2.00e-02 2.50e+03 8.29e+01 bond pdb=" C28 JER D 401 " pdb=" C29 JER D 401 " ideal model delta sigma weight residual 1.532 1.354 0.178 2.00e-02 2.50e+03 7.88e+01 bond pdb=" C28 JER D 401 " pdb=" C32 JER D 401 " ideal model delta sigma weight residual 1.537 1.651 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C10 JER D 401 " pdb=" C15 JER D 401 " ideal model delta sigma weight residual 1.460 1.374 0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C22 JER D 401 " pdb=" O23 JER D 401 " ideal model delta sigma weight residual 1.332 1.410 -0.078 2.00e-02 2.50e+03 1.53e+01 ... (remaining 9250 not shown) Histogram of bond angle deviations from ideal: 99.99 - 106.79: 188 106.79 - 113.59: 5102 113.59 - 120.39: 3483 120.39 - 127.19: 3634 127.19 - 133.99: 93 Bond angle restraints: 12500 Sorted by residual: angle pdb=" N PHE D 237 " pdb=" CA PHE D 237 " pdb=" C PHE D 237 " ideal model delta sigma weight residual 111.36 123.07 -11.71 1.09e+00 8.42e-01 1.15e+02 angle pdb=" N ARG D 238 " pdb=" CA ARG D 238 " pdb=" C ARG D 238 " ideal model delta sigma weight residual 113.16 123.13 -9.97 1.24e+00 6.50e-01 6.46e+01 angle pdb=" N LYS D 239 " pdb=" CA LYS D 239 " pdb=" C LYS D 239 " ideal model delta sigma weight residual 110.23 116.35 -6.12 1.45e+00 4.76e-01 1.78e+01 angle pdb=" N THR D 236 " pdb=" CA THR D 236 " pdb=" C THR D 236 " ideal model delta sigma weight residual 109.54 103.76 5.78 1.37e+00 5.33e-01 1.78e+01 angle pdb=" C26 JER D 401 " pdb=" C28 JER D 401 " pdb=" C29 JER D 401 " ideal model delta sigma weight residual 114.08 102.52 11.56 3.00e+00 1.11e-01 1.48e+01 ... (remaining 12495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5012 17.98 - 35.95: 429 35.95 - 53.93: 65 53.93 - 71.91: 11 71.91 - 89.88: 6 Dihedral angle restraints: 5523 sinusoidal: 2203 harmonic: 3320 Sorted by residual: dihedral pdb=" CB CYS D 184 " pdb=" SG CYS D 184 " pdb=" SG CYS D 191 " pdb=" CB CYS D 191 " ideal model delta sinusoidal sigma weight residual -86.00 -47.75 -38.25 1 1.00e+01 1.00e-02 2.06e+01 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 65.20 27.80 1 1.00e+01 1.00e-02 1.11e+01 dihedral pdb=" CA ASP A 229 " pdb=" CB ASP A 229 " pdb=" CG ASP A 229 " pdb=" OD1 ASP A 229 " ideal model delta sinusoidal sigma weight residual -30.00 -87.29 57.29 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 5520 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1357 0.093 - 0.186: 62 0.186 - 0.280: 4 0.280 - 0.373: 0 0.373 - 0.466: 1 Chirality restraints: 1424 Sorted by residual: chirality pdb=" CA PHE D 237 " pdb=" N PHE D 237 " pdb=" C PHE D 237 " pdb=" CB PHE D 237 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" CA GLU D 249 " pdb=" N GLU D 249 " pdb=" C GLU D 249 " pdb=" CB GLU D 249 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA SER D 251 " pdb=" N SER D 251 " pdb=" C SER D 251 " pdb=" CB SER D 251 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1421 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 235 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO E 236 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO C 49 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 239 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.24e+00 pdb=" C LYS D 239 " -0.026 2.00e-02 2.50e+03 pdb=" O LYS D 239 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN D 240 " 0.009 2.00e-02 2.50e+03 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 289 2.71 - 3.26: 8647 3.26 - 3.80: 13775 3.80 - 4.35: 16940 4.35 - 4.90: 30045 Nonbonded interactions: 69696 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.160 2.440 nonbonded pdb=" OG SER D 192 " pdb=" O LEU D 195 " model vdw 2.180 2.440 nonbonded pdb=" OD2 ASP A 341 " pdb=" NZ LYS D 239 " model vdw 2.206 2.520 nonbonded pdb=" O THR D 236 " pdb=" OG1 THR D 236 " model vdw 2.218 2.440 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.259 2.440 ... (remaining 69691 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 4.090 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 27.820 Find NCS groups from input model: 0.210 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 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 0.182 9255 Z= 0.275 Angle : 0.585 11.711 12500 Z= 0.336 Chirality : 0.043 0.466 1424 Planarity : 0.003 0.053 1557 Dihedral : 13.326 89.882 3372 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.30 % Allowed : 5.18 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.23), residues: 1126 helix: 0.22 (0.24), residues: 382 sheet: -1.46 (0.29), residues: 277 loop : -2.53 (0.23), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 176 HIS 0.003 0.000 HIS D 199 PHE 0.020 0.001 PHE E 108 TYR 0.014 0.001 TYR E 190 ARG 0.004 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 152 time to evaluate : 1.039 Fit side-chains REVERT: A 275 GLU cc_start: 0.8062 (tp30) cc_final: 0.7848 (mm-30) REVERT: B 44 GLN cc_start: 0.7721 (tp40) cc_final: 0.7430 (mt0) REVERT: B 137 ARG cc_start: 0.7464 (tpp-160) cc_final: 0.6979 (tpt90) REVERT: B 197 ARG cc_start: 0.7291 (tpp80) cc_final: 0.7004 (tpp80) REVERT: B 217 MET cc_start: 0.7100 (ptt) cc_final: 0.6529 (ptm) REVERT: B 274 THR cc_start: 0.8559 (m) cc_final: 0.8235 (p) REVERT: B 280 LYS cc_start: 0.8172 (tptp) cc_final: 0.7920 (tptt) REVERT: B 289 TYR cc_start: 0.8866 (m-80) cc_final: 0.7606 (m-80) REVERT: B 292 PHE cc_start: 0.8510 (m-10) cc_final: 0.8252 (m-10) REVERT: B 312 ASP cc_start: 0.8438 (t0) cc_final: 0.8035 (t0) REVERT: D 190 SER cc_start: 0.6529 (m) cc_final: 0.6206 (t) REVERT: D 224 ILE cc_start: 0.6056 (tt) cc_final: 0.5765 (tt) REVERT: D 292 ARG cc_start: 0.8190 (mtt90) cc_final: 0.7508 (mtm180) REVERT: E 93 MET cc_start: 0.6976 (ttm) cc_final: 0.6028 (ttm) REVERT: E 192 MET cc_start: 0.5588 (tpp) cc_final: 0.4274 (ptp) outliers start: 3 outliers final: 2 residues processed: 155 average time/residue: 0.2788 time to fit residues: 55.7356 Evaluate side-chains 122 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 120 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 249 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 0.2980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 75 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 HIS D 240 ASN E 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9255 Z= 0.151 Angle : 0.483 7.492 12500 Z= 0.246 Chirality : 0.039 0.152 1424 Planarity : 0.003 0.055 1557 Dihedral : 5.742 68.035 1320 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.12 % Allowed : 12.18 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.24), residues: 1126 helix: 1.57 (0.26), residues: 379 sheet: -1.03 (0.31), residues: 277 loop : -2.14 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 176 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE E 108 TYR 0.016 0.001 TYR E 190 ARG 0.005 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8104 (tp30) cc_final: 0.7902 (mm-30) REVERT: B 197 ARG cc_start: 0.7310 (tpp80) cc_final: 0.7075 (tpp80) REVERT: B 217 MET cc_start: 0.7218 (ptt) cc_final: 0.6733 (ptm) REVERT: B 274 THR cc_start: 0.8584 (m) cc_final: 0.8357 (p) REVERT: B 280 LYS cc_start: 0.8187 (tptp) cc_final: 0.7979 (tptt) REVERT: B 289 TYR cc_start: 0.8845 (m-80) cc_final: 0.7577 (m-80) REVERT: B 292 PHE cc_start: 0.8483 (m-10) cc_final: 0.8258 (m-10) REVERT: B 312 ASP cc_start: 0.8397 (t0) cc_final: 0.7969 (t0) REVERT: D 224 ILE cc_start: 0.6220 (tt) cc_final: 0.5935 (tt) REVERT: E 82 GLN cc_start: 0.7259 (tp-100) cc_final: 0.6873 (tp40) REVERT: E 93 MET cc_start: 0.7050 (ttm) cc_final: 0.6032 (ttm) REVERT: E 140 MET cc_start: 0.8667 (mmm) cc_final: 0.8279 (mmm) outliers start: 11 outliers final: 8 residues processed: 128 average time/residue: 0.2778 time to fit residues: 46.6784 Evaluate side-chains 125 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.0970 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN D 303 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9255 Z= 0.232 Angle : 0.522 7.627 12500 Z= 0.268 Chirality : 0.041 0.177 1424 Planarity : 0.004 0.063 1557 Dihedral : 5.815 73.741 1316 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.54 % Allowed : 14.21 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.25), residues: 1126 helix: 2.09 (0.27), residues: 378 sheet: -0.86 (0.31), residues: 279 loop : -1.97 (0.25), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 176 HIS 0.004 0.001 HIS B 62 PHE 0.016 0.001 PHE A 189 TYR 0.019 0.002 TYR E 235 ARG 0.005 0.000 ARG D 324 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 247 MET cc_start: 0.8585 (mtp) cc_final: 0.8262 (mtp) REVERT: A 275 GLU cc_start: 0.8227 (tp30) cc_final: 0.7985 (tp30) REVERT: B 217 MET cc_start: 0.7253 (ptt) cc_final: 0.6781 (ptm) REVERT: B 274 THR cc_start: 0.8660 (m) cc_final: 0.8361 (p) REVERT: B 280 LYS cc_start: 0.8268 (tptp) cc_final: 0.8029 (tptt) REVERT: B 312 ASP cc_start: 0.8427 (t0) cc_final: 0.7989 (t0) REVERT: D 151 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6627 (tt) REVERT: D 190 SER cc_start: 0.6499 (m) cc_final: 0.6038 (t) REVERT: E 82 GLN cc_start: 0.7240 (tp-100) cc_final: 0.6869 (tp40) REVERT: E 140 MET cc_start: 0.8659 (mmm) cc_final: 0.8228 (mmm) outliers start: 25 outliers final: 16 residues processed: 146 average time/residue: 0.2717 time to fit residues: 52.0757 Evaluate side-chains 143 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 108 optimal weight: 0.0670 chunk 53 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 0.0270 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 32 GLN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9255 Z= 0.233 Angle : 0.522 8.045 12500 Z= 0.267 Chirality : 0.041 0.172 1424 Planarity : 0.004 0.061 1557 Dihedral : 5.835 73.570 1316 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.05 % Allowed : 17.46 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.25), residues: 1126 helix: 2.27 (0.26), residues: 377 sheet: -0.82 (0.31), residues: 279 loop : -1.92 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.016 0.001 PHE E 108 TYR 0.023 0.002 TYR E 235 ARG 0.005 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8209 (tp30) cc_final: 0.7917 (tp30) REVERT: B 217 MET cc_start: 0.7281 (ptt) cc_final: 0.6810 (ptm) REVERT: B 259 GLN cc_start: 0.7837 (tt0) cc_final: 0.7422 (tt0) REVERT: B 274 THR cc_start: 0.8664 (m) cc_final: 0.8379 (p) REVERT: B 280 LYS cc_start: 0.8267 (tptp) cc_final: 0.8064 (tptt) REVERT: B 312 ASP cc_start: 0.8372 (t0) cc_final: 0.8085 (t0) REVERT: D 190 SER cc_start: 0.7117 (m) cc_final: 0.6604 (t) REVERT: D 227 LEU cc_start: 0.6735 (OUTLIER) cc_final: 0.6498 (mp) REVERT: E 82 GLN cc_start: 0.7261 (tp-100) cc_final: 0.6796 (tp40) REVERT: E 140 MET cc_start: 0.8652 (mmm) cc_final: 0.8215 (mmm) REVERT: E 177 PHE cc_start: 0.6265 (OUTLIER) cc_final: 0.5598 (p90) outliers start: 30 outliers final: 21 residues processed: 144 average time/residue: 0.2324 time to fit residues: 44.6504 Evaluate side-chains 144 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9255 Z= 0.226 Angle : 0.527 8.632 12500 Z= 0.267 Chirality : 0.040 0.173 1424 Planarity : 0.004 0.062 1557 Dihedral : 5.870 73.828 1316 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.15 % Allowed : 19.19 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.25), residues: 1126 helix: 2.38 (0.27), residues: 377 sheet: -0.86 (0.31), residues: 279 loop : -1.87 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS D 199 PHE 0.017 0.001 PHE E 108 TYR 0.025 0.002 TYR E 235 ARG 0.006 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 1.064 Fit side-chains REVERT: A 275 GLU cc_start: 0.8206 (tp30) cc_final: 0.7910 (tp30) REVERT: B 19 ARG cc_start: 0.7647 (ttp-170) cc_final: 0.7397 (ttp-170) REVERT: B 217 MET cc_start: 0.7290 (ptt) cc_final: 0.6815 (ptm) REVERT: B 259 GLN cc_start: 0.7813 (tt0) cc_final: 0.7400 (tt0) REVERT: B 274 THR cc_start: 0.8662 (m) cc_final: 0.8387 (p) REVERT: B 280 LYS cc_start: 0.8287 (tptp) cc_final: 0.8086 (tptt) REVERT: B 312 ASP cc_start: 0.8362 (t0) cc_final: 0.8109 (t0) REVERT: D 190 SER cc_start: 0.7163 (m) cc_final: 0.6696 (t) REVERT: E 82 GLN cc_start: 0.7173 (tp-100) cc_final: 0.6675 (tp40) REVERT: E 163 LYS cc_start: 0.6993 (tttt) cc_final: 0.6649 (ttmt) REVERT: E 177 PHE cc_start: 0.6287 (OUTLIER) cc_final: 0.5611 (p90) outliers start: 31 outliers final: 25 residues processed: 149 average time/residue: 0.2544 time to fit residues: 50.4248 Evaluate side-chains 151 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 125 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 108 optimal weight: 10.0000 chunk 89 optimal weight: 0.0980 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.0870 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9255 Z= 0.122 Angle : 0.468 6.848 12500 Z= 0.238 Chirality : 0.039 0.158 1424 Planarity : 0.003 0.059 1557 Dihedral : 5.858 68.861 1316 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.93 % Allowed : 21.02 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.25), residues: 1126 helix: 2.58 (0.27), residues: 380 sheet: -0.76 (0.31), residues: 279 loop : -1.75 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.003 0.000 HIS D 199 PHE 0.017 0.001 PHE E 108 TYR 0.022 0.001 TYR E 235 ARG 0.006 0.000 ARG D 324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 1.050 Fit side-chains REVERT: A 275 GLU cc_start: 0.8154 (tp30) cc_final: 0.7775 (tp30) REVERT: B 19 ARG cc_start: 0.7651 (ttp-170) cc_final: 0.7405 (ttp-170) REVERT: B 172 GLU cc_start: 0.8330 (tt0) cc_final: 0.8112 (tt0) REVERT: B 189 SER cc_start: 0.8140 (m) cc_final: 0.7898 (m) REVERT: B 259 GLN cc_start: 0.7853 (tt0) cc_final: 0.7469 (tt0) REVERT: B 280 LYS cc_start: 0.8232 (tptp) cc_final: 0.8030 (tptt) REVERT: B 289 TYR cc_start: 0.8847 (m-80) cc_final: 0.7439 (m-80) REVERT: B 312 ASP cc_start: 0.8331 (t0) cc_final: 0.8077 (t0) REVERT: D 190 SER cc_start: 0.7152 (m) cc_final: 0.6710 (t) REVERT: E 82 GLN cc_start: 0.7250 (tp-100) cc_final: 0.6775 (tp40) REVERT: E 163 LYS cc_start: 0.6981 (tttt) cc_final: 0.6684 (ttmt) REVERT: E 192 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.4579 (ptp) outliers start: 19 outliers final: 16 residues processed: 138 average time/residue: 0.2609 time to fit residues: 47.5171 Evaluate side-chains 138 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9255 Z= 0.183 Angle : 0.503 8.423 12500 Z= 0.254 Chirality : 0.040 0.170 1424 Planarity : 0.004 0.061 1557 Dihedral : 5.847 67.313 1316 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.15 % Allowed : 20.51 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.25), residues: 1126 helix: 2.64 (0.26), residues: 377 sheet: -0.75 (0.31), residues: 279 loop : -1.71 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS E 35 PHE 0.017 0.001 PHE E 108 TYR 0.023 0.001 TYR E 235 ARG 0.007 0.000 ARG D 324 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 1.037 Fit side-chains REVERT: A 275 GLU cc_start: 0.8154 (tp30) cc_final: 0.7843 (tp30) REVERT: B 19 ARG cc_start: 0.7697 (ttp-170) cc_final: 0.7456 (ttp-170) REVERT: B 172 GLU cc_start: 0.8338 (tt0) cc_final: 0.8122 (tt0) REVERT: B 217 MET cc_start: 0.7353 (ptt) cc_final: 0.6904 (ptm) REVERT: B 259 GLN cc_start: 0.7864 (tt0) cc_final: 0.7461 (tt0) REVERT: B 289 TYR cc_start: 0.8881 (m-80) cc_final: 0.7525 (m-80) REVERT: B 312 ASP cc_start: 0.8311 (t0) cc_final: 0.8070 (t0) REVERT: D 190 SER cc_start: 0.7191 (m) cc_final: 0.6797 (t) REVERT: E 82 GLN cc_start: 0.7261 (tp-100) cc_final: 0.6775 (tp40) REVERT: E 163 LYS cc_start: 0.7033 (tttt) cc_final: 0.6687 (ttmt) REVERT: E 177 PHE cc_start: 0.6164 (OUTLIER) cc_final: 0.5623 (p90) REVERT: E 192 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.4532 (ptp) outliers start: 31 outliers final: 24 residues processed: 146 average time/residue: 0.2497 time to fit residues: 48.4232 Evaluate side-chains 150 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 124 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN E 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9255 Z= 0.215 Angle : 0.516 6.944 12500 Z= 0.264 Chirality : 0.040 0.176 1424 Planarity : 0.004 0.062 1557 Dihedral : 6.031 68.991 1316 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.94 % Allowed : 20.91 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.25), residues: 1126 helix: 2.64 (0.26), residues: 377 sheet: -0.87 (0.31), residues: 280 loop : -1.67 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS D 199 PHE 0.017 0.001 PHE E 108 TYR 0.025 0.001 TYR E 235 ARG 0.007 0.000 ARG D 324 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 122 time to evaluate : 1.083 Fit side-chains REVERT: A 275 GLU cc_start: 0.8183 (tp30) cc_final: 0.7935 (tp30) REVERT: B 19 ARG cc_start: 0.7713 (ttp-170) cc_final: 0.7474 (ttp-170) REVERT: B 172 GLU cc_start: 0.8397 (tt0) cc_final: 0.8193 (tt0) REVERT: B 217 MET cc_start: 0.7368 (ptt) cc_final: 0.6907 (ptm) REVERT: B 259 GLN cc_start: 0.7835 (tt0) cc_final: 0.7418 (tt0) REVERT: B 312 ASP cc_start: 0.8309 (t0) cc_final: 0.8094 (t0) REVERT: D 190 SER cc_start: 0.7176 (m) cc_final: 0.6827 (t) REVERT: E 82 GLN cc_start: 0.7219 (tp-100) cc_final: 0.6706 (tp40) REVERT: E 163 LYS cc_start: 0.7041 (tttt) cc_final: 0.6673 (ttmt) REVERT: E 177 PHE cc_start: 0.6219 (OUTLIER) cc_final: 0.5527 (p90) REVERT: E 192 MET cc_start: 0.6727 (OUTLIER) cc_final: 0.4558 (ptp) outliers start: 29 outliers final: 25 residues processed: 141 average time/residue: 0.2583 time to fit residues: 48.3039 Evaluate side-chains 146 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9255 Z= 0.173 Angle : 0.497 7.054 12500 Z= 0.255 Chirality : 0.039 0.166 1424 Planarity : 0.004 0.057 1557 Dihedral : 5.888 66.856 1316 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.94 % Allowed : 21.32 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.25), residues: 1126 helix: 2.67 (0.26), residues: 380 sheet: -0.75 (0.31), residues: 275 loop : -1.66 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS D 199 PHE 0.017 0.001 PHE E 108 TYR 0.025 0.001 TYR E 235 ARG 0.008 0.000 ARG D 324 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 1.005 Fit side-chains REVERT: A 32 ARG cc_start: 0.8434 (ptp-110) cc_final: 0.8049 (mtm110) REVERT: B 19 ARG cc_start: 0.7721 (ttp-170) cc_final: 0.7485 (ttp-170) REVERT: B 172 GLU cc_start: 0.8344 (tt0) cc_final: 0.8138 (tt0) REVERT: B 217 MET cc_start: 0.7505 (ptt) cc_final: 0.7028 (ptm) REVERT: B 234 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7716 (t80) REVERT: B 259 GLN cc_start: 0.7866 (tt0) cc_final: 0.7448 (tt0) REVERT: B 289 TYR cc_start: 0.8886 (m-80) cc_final: 0.7525 (m-80) REVERT: B 312 ASP cc_start: 0.8316 (t0) cc_final: 0.8105 (t0) REVERT: D 190 SER cc_start: 0.7198 (m) cc_final: 0.6879 (t) REVERT: E 82 GLN cc_start: 0.7220 (tp-100) cc_final: 0.6705 (tp40) REVERT: E 163 LYS cc_start: 0.7076 (tttt) cc_final: 0.6712 (ttmt) REVERT: E 177 PHE cc_start: 0.6189 (OUTLIER) cc_final: 0.5661 (p90) REVERT: E 192 MET cc_start: 0.6648 (OUTLIER) cc_final: 0.4521 (ptp) outliers start: 29 outliers final: 23 residues processed: 135 average time/residue: 0.2570 time to fit residues: 46.2101 Evaluate side-chains 141 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 40.0000 chunk 88 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9255 Z= 0.184 Angle : 0.503 7.186 12500 Z= 0.258 Chirality : 0.040 0.167 1424 Planarity : 0.004 0.061 1557 Dihedral : 5.820 65.737 1316 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.84 % Allowed : 21.12 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.25), residues: 1126 helix: 2.69 (0.26), residues: 376 sheet: -0.74 (0.31), residues: 275 loop : -1.65 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS E 35 PHE 0.016 0.001 PHE E 108 TYR 0.024 0.001 TYR E 235 ARG 0.009 0.000 ARG D 324 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 1.038 Fit side-chains REVERT: A 32 ARG cc_start: 0.8413 (ptp-110) cc_final: 0.8031 (mtm110) REVERT: B 19 ARG cc_start: 0.7726 (ttp-170) cc_final: 0.7491 (ttp-170) REVERT: B 118 ASP cc_start: 0.7943 (t0) cc_final: 0.7632 (t0) REVERT: B 172 GLU cc_start: 0.8410 (tt0) cc_final: 0.8198 (tt0) REVERT: B 217 MET cc_start: 0.7513 (ptt) cc_final: 0.7031 (ptm) REVERT: B 234 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7721 (t80) REVERT: B 259 GLN cc_start: 0.7858 (tt0) cc_final: 0.7444 (tt0) REVERT: B 289 TYR cc_start: 0.8890 (m-80) cc_final: 0.7520 (m-80) REVERT: E 82 GLN cc_start: 0.7222 (tp-100) cc_final: 0.6706 (tp40) REVERT: E 163 LYS cc_start: 0.7088 (tttt) cc_final: 0.6715 (ttmt) REVERT: E 177 PHE cc_start: 0.6213 (OUTLIER) cc_final: 0.5683 (p90) REVERT: E 192 MET cc_start: 0.6616 (OUTLIER) cc_final: 0.4525 (ptp) outliers start: 28 outliers final: 23 residues processed: 133 average time/residue: 0.2414 time to fit residues: 43.0407 Evaluate side-chains 139 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 113 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 0.0030 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.167927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.109548 restraints weight = 10044.323| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.45 r_work: 0.3156 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9255 Z= 0.196 Angle : 0.513 7.118 12500 Z= 0.262 Chirality : 0.040 0.169 1424 Planarity : 0.004 0.059 1557 Dihedral : 5.827 66.488 1316 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.74 % Allowed : 21.12 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.25), residues: 1126 helix: 2.68 (0.26), residues: 376 sheet: -0.78 (0.31), residues: 275 loop : -1.66 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS E 35 PHE 0.015 0.001 PHE E 108 TYR 0.024 0.001 TYR E 235 ARG 0.008 0.000 ARG D 324 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2211.47 seconds wall clock time: 41 minutes 33.29 seconds (2493.29 seconds total)