Starting phenix.real_space_refine on Tue Feb 13 23:20:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f58_31461/02_2024/7f58_31461_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f58_31461/02_2024/7f58_31461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f58_31461/02_2024/7f58_31461.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f58_31461/02_2024/7f58_31461.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f58_31461/02_2024/7f58_31461_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f58_31461/02_2024/7f58_31461_updated.pdb" } resolution = 3.1 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= 0.005 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 S 62 5.16 5 Cl 1 4.86 5 C 5112 2.51 5 N 1389 2.21 5 O 1500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 42": "OE1" <-> "OE2" Residue "R PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 315": "OE1" <-> "OE2" Residue "A GLU 16": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8065 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2133 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 7, 'TRANS': 265} Chain breaks: 2 Chain: "A" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1885 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 49 Unusual residues: {' CA': 1, '1I8': 1} Classifications: {'undetermined': 2, 'water': 6} Link IDs: {None: 7} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.90, per 1000 atoms: 0.61 Number of scatterers: 8065 At special positions: 0 Unit cell: (86.19, 96.33, 122.694, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 Cl 1 17.00 S 62 16.00 O 1500 8.00 N 1389 7.00 C 5112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 40 " - pdb=" SG CYS R 279 " distance=2.03 Simple disulfide: pdb=" SG CYS R 271 " - pdb=" SG CYS R 277 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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: 3.35 Conformation dependent library (CDL) restraints added in 1.6 seconds 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 11 sheets defined 40.0% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'R' and resid 48 through 70 Processing helix chain 'R' and resid 78 through 109 Processing helix chain 'R' and resid 118 through 152 removed outlier: 4.051A pdb=" N ASN R 123 " --> pdb=" O VAL R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 160 No H-bonds generated for 'chain 'R' and resid 157 through 160' Processing helix chain 'R' and resid 163 through 186 Processing helix chain 'R' and resid 191 through 227 removed outlier: 3.783A pdb=" N ILE R 198 " --> pdb=" O ILE R 194 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR R 199 " --> pdb=" O ILE R 195 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N MET R 200 " --> pdb=" O CYS R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 239 through 270 removed outlier: 3.813A pdb=" N PHE R 254 " --> pdb=" O LEU R 250 " (cutoff:3.500A) Proline residue: R 260 - end of helix Processing helix chain 'R' and resid 275 through 301 removed outlier: 4.575A pdb=" N HIS R 283 " --> pdb=" O CYS R 279 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N PHE R 284 " --> pdb=" O PHE R 280 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASN R 285 " --> pdb=" O MET R 281 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU R 286 " --> pdb=" O SER R 282 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE R 296 " --> pdb=" O MET R 292 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 303 through 305 No H-bonds generated for 'chain 'R' and resid 303 through 305' Processing helix chain 'R' and resid 307 through 319 Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.584A pdb=" N LYS A 17 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG A 38 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.978A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 390 removed outlier: 3.776A pdb=" N ASN A 377 " --> pdb=" O ARG A 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.705A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 34 through 36 No H-bonds generated for 'chain 'B' and resid 34 through 36' Processing helix chain 'G' and resid 7 through 23 removed outlier: 4.173A pdb=" N ARG G 13 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.438A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.740A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.010A 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: 6.907A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.241A 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: 6.708A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.814A 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: 7.027A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.161A 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: 6.662A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.405A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 317 through 320 removed outlier: 3.557A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 18 through 20 removed outlier: 3.739A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.964A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1008 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: 2.23 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1313 1.31 - 1.44: 2213 1.44 - 1.57: 4594 1.57 - 1.70: 5 1.70 - 1.82: 88 Bond restraints: 8213 Sorted by residual: bond pdb=" C33 1I8 R 601 " pdb=" C38 1I8 R 601 " ideal model delta sigma weight residual 1.388 1.572 -0.184 2.00e-02 2.50e+03 8.48e+01 bond pdb=" C28 1I8 R 601 " pdb=" N07 1I8 R 601 " ideal model delta sigma weight residual 1.337 1.512 -0.175 2.00e-02 2.50e+03 7.69e+01 bond pdb=" C35 1I8 R 601 " pdb=" C39 1I8 R 601 " ideal model delta sigma weight residual 1.387 1.562 -0.175 2.00e-02 2.50e+03 7.66e+01 bond pdb=" C39 1I8 R 601 " pdb=" C42 1I8 R 601 " ideal model delta sigma weight residual 1.390 1.564 -0.174 2.00e-02 2.50e+03 7.61e+01 bond pdb=" C31 1I8 R 601 " pdb=" C36 1I8 R 601 " ideal model delta sigma weight residual 1.386 1.549 -0.163 2.00e-02 2.50e+03 6.68e+01 ... (remaining 8208 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.89: 134 105.89 - 112.92: 4424 112.92 - 119.95: 2792 119.95 - 126.98: 3686 126.98 - 134.02: 84 Bond angle restraints: 11120 Sorted by residual: angle pdb=" N SER B 316 " pdb=" CA SER B 316 " pdb=" C SER B 316 " ideal model delta sigma weight residual 111.28 121.24 -9.96 1.09e+00 8.42e-01 8.34e+01 angle pdb=" N LYS B 78 " pdb=" CA LYS B 78 " pdb=" C LYS B 78 " ideal model delta sigma weight residual 108.13 116.75 -8.62 1.72e+00 3.38e-01 2.51e+01 angle pdb=" N VAL B 315 " pdb=" CA VAL B 315 " pdb=" C VAL B 315 " ideal model delta sigma weight residual 106.21 111.01 -4.80 1.07e+00 8.73e-01 2.01e+01 angle pdb=" CA PRO R 299 " pdb=" N PRO R 299 " pdb=" CD PRO R 299 " ideal model delta sigma weight residual 112.00 105.87 6.13 1.40e+00 5.10e-01 1.92e+01 angle pdb=" N PRO N 100 " pdb=" CA PRO N 100 " pdb=" C PRO N 100 " ideal model delta sigma weight residual 113.53 118.74 -5.21 1.39e+00 5.18e-01 1.41e+01 ... (remaining 11115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.97: 4691 21.97 - 43.94: 199 43.94 - 65.92: 44 65.92 - 87.89: 9 87.89 - 109.86: 3 Dihedral angle restraints: 4946 sinusoidal: 1974 harmonic: 2972 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -13.19 -72.81 1 1.00e+01 1.00e-02 6.76e+01 dihedral pdb=" CB CYS R 40 " pdb=" SG CYS R 40 " pdb=" SG CYS R 279 " pdb=" CB CYS R 279 " ideal model delta sinusoidal sigma weight residual -86.00 -40.19 -45.81 1 1.00e+01 1.00e-02 2.91e+01 dihedral pdb=" N07 1I8 R 601 " pdb=" C28 1I8 R 601 " pdb=" C29 1I8 R 601 " pdb=" N09 1I8 R 601 " ideal model delta sinusoidal sigma weight residual -1.56 108.30 -109.86 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 4943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1008 0.056 - 0.112: 219 0.112 - 0.168: 37 0.168 - 0.225: 5 0.225 - 0.281: 2 Chirality restraints: 1271 Sorted by residual: chirality pdb=" CB ILE R 194 " pdb=" CA ILE R 194 " pdb=" CG1 ILE R 194 " pdb=" CG2 ILE R 194 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA SER B 316 " pdb=" N SER B 316 " pdb=" C SER B 316 " pdb=" CB SER B 316 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PRO N 100 " pdb=" N PRO N 100 " pdb=" C PRO N 100 " pdb=" CB PRO N 100 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1268 not shown) Planarity restraints: 1410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP R 298 " -0.096 5.00e-02 4.00e+02 1.43e-01 3.28e+01 pdb=" N PRO R 299 " 0.248 5.00e-02 4.00e+02 pdb=" CA PRO R 299 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO R 299 " -0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 374 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C ARG A 374 " 0.064 2.00e-02 2.50e+03 pdb=" O ARG A 374 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL A 375 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 126 " 0.015 2.00e-02 2.50e+03 2.92e-02 8.53e+00 pdb=" C ASP R 126 " -0.051 2.00e-02 2.50e+03 pdb=" O ASP R 126 " 0.019 2.00e-02 2.50e+03 pdb=" N SER R 127 " 0.017 2.00e-02 2.50e+03 ... (remaining 1407 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2171 2.80 - 3.33: 7763 3.33 - 3.85: 13705 3.85 - 4.38: 16569 4.38 - 4.90: 28041 Nonbonded interactions: 68249 Sorted by model distance: nonbonded pdb=" NH1 ARG R 305 " pdb=" OE2 GLU A 392 " model vdw 2.279 2.520 nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.290 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.299 2.440 nonbonded pdb=" NH2 ARG B 256 " pdb=" OD2 ASP G 36 " model vdw 2.301 2.520 nonbonded pdb=" OE1 GLN A 236 " pdb=" NH1 ARG B 314 " model vdw 2.310 2.520 ... (remaining 68244 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.070 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.400 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 : 0.008 0.184 8213 Z= 0.506 Angle : 0.790 9.956 11120 Z= 0.467 Chirality : 0.049 0.281 1271 Planarity : 0.006 0.143 1410 Dihedral : 13.303 109.858 3008 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.50 % Favored : 97.40 % Rotamer: Outliers : 0.23 % Allowed : 4.09 % Favored : 95.68 % 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: 0.89 (0.26), residues: 1001 helix: 0.84 (0.24), residues: 405 sheet: 0.88 (0.36), residues: 211 loop : 0.35 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 82 HIS 0.009 0.002 HIS A 357 PHE 0.021 0.002 PHE R 262 TYR 0.020 0.002 TYR A 339 ARG 0.008 0.001 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 207 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: R 215 MET cc_start: 0.8368 (mtp) cc_final: 0.8129 (mtm) REVERT: R 220 ARG cc_start: 0.7076 (ttp80) cc_final: 0.6754 (ttp-170) REVERT: R 309 LEU cc_start: 0.7564 (mt) cc_final: 0.7269 (tt) REVERT: B 61 MET cc_start: 0.7152 (tmm) cc_final: 0.6904 (ttp) REVERT: B 186 ASP cc_start: 0.7380 (m-30) cc_final: 0.7040 (m-30) REVERT: B 325 MET cc_start: 0.7518 (mmm) cc_final: 0.7179 (mmt) REVERT: N 108 PHE cc_start: 0.6715 (OUTLIER) cc_final: 0.5738 (m-80) outliers start: 2 outliers final: 0 residues processed: 208 average time/residue: 0.2466 time to fit residues: 65.5822 Evaluate side-chains 157 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 108 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 294 ASN A 357 HIS B 9 GLN B 16 ASN B 32 GLN B 132 ASN B 176 GLN B 259 GLN N 3 GLN N 13 GLN N 77 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8213 Z= 0.226 Angle : 0.551 7.722 11120 Z= 0.303 Chirality : 0.043 0.154 1271 Planarity : 0.005 0.079 1410 Dihedral : 7.166 102.060 1161 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.93 % Allowed : 7.84 % Favored : 90.23 % 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: 1.31 (0.26), residues: 1001 helix: 1.49 (0.24), residues: 407 sheet: 0.65 (0.34), residues: 215 loop : 0.50 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.002 PHE N 68 TYR 0.018 0.001 TYR A 339 ARG 0.003 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 158 time to evaluate : 0.861 Fit side-chains REVERT: R 215 MET cc_start: 0.8381 (mtp) cc_final: 0.8156 (mtm) REVERT: A 343 ASP cc_start: 0.7642 (m-30) cc_final: 0.7202 (m-30) REVERT: B 59 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.8152 (t80) REVERT: B 97 SER cc_start: 0.8271 (p) cc_final: 0.7887 (m) REVERT: B 186 ASP cc_start: 0.7386 (m-30) cc_final: 0.7138 (m-30) REVERT: B 226 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7414 (mt-10) REVERT: B 254 ASP cc_start: 0.7851 (p0) cc_final: 0.7500 (t0) REVERT: G 47 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7251 (mt-10) outliers start: 17 outliers final: 11 residues processed: 167 average time/residue: 0.2502 time to fit residues: 55.1070 Evaluate side-chains 155 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 97 optimal weight: 0.0970 chunk 80 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 overall best weight: 1.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8213 Z= 0.197 Angle : 0.500 7.833 11120 Z= 0.274 Chirality : 0.041 0.179 1271 Planarity : 0.005 0.062 1410 Dihedral : 6.769 99.519 1159 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.16 % Allowed : 8.41 % Favored : 89.43 % 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: 1.38 (0.26), residues: 1001 helix: 1.55 (0.25), residues: 409 sheet: 0.63 (0.34), residues: 224 loop : 0.55 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.007 0.001 HIS A 357 PHE 0.018 0.002 PHE N 108 TYR 0.016 0.001 TYR A 339 ARG 0.003 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 156 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 343 ASP cc_start: 0.7632 (m-30) cc_final: 0.7225 (m-30) REVERT: B 59 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.8240 (t80) REVERT: B 226 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7373 (mt-10) outliers start: 19 outliers final: 15 residues processed: 166 average time/residue: 0.2330 time to fit residues: 50.9656 Evaluate side-chains 158 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 47 optimal weight: 0.0470 chunk 85 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8213 Z= 0.219 Angle : 0.498 7.313 11120 Z= 0.272 Chirality : 0.041 0.172 1271 Planarity : 0.005 0.057 1410 Dihedral : 6.684 95.900 1159 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.73 % Allowed : 9.66 % Favored : 87.61 % 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: 1.21 (0.26), residues: 1001 helix: 1.48 (0.25), residues: 409 sheet: 0.65 (0.34), residues: 217 loop : 0.31 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.007 0.001 HIS A 357 PHE 0.020 0.002 PHE N 108 TYR 0.017 0.001 TYR A 339 ARG 0.002 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: R 280 PHE cc_start: 0.7934 (t80) cc_final: 0.7531 (t80) REVERT: A 343 ASP cc_start: 0.7688 (m-30) cc_final: 0.7304 (m-30) REVERT: B 59 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.8270 (t80) outliers start: 24 outliers final: 18 residues processed: 160 average time/residue: 0.2229 time to fit residues: 47.3962 Evaluate side-chains 152 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 81 optimal weight: 0.0050 chunk 66 optimal weight: 8.9990 chunk 0 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 85 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8213 Z= 0.142 Angle : 0.447 7.231 11120 Z= 0.246 Chirality : 0.040 0.152 1271 Planarity : 0.004 0.055 1410 Dihedral : 6.454 92.682 1159 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.50 % Allowed : 11.36 % Favored : 86.14 % 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: 1.28 (0.26), residues: 1001 helix: 1.59 (0.25), residues: 411 sheet: 0.55 (0.34), residues: 214 loop : 0.36 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE R 262 TYR 0.012 0.001 TYR A 339 ARG 0.002 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.5987 (OUTLIER) cc_final: 0.5350 (mm) REVERT: B 59 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.8277 (t80) outliers start: 22 outliers final: 16 residues processed: 156 average time/residue: 0.2328 time to fit residues: 47.5067 Evaluate side-chains 150 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 74 ASN A 23 ASN A 371 ASN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8213 Z= 0.404 Angle : 0.604 7.178 11120 Z= 0.326 Chirality : 0.045 0.208 1271 Planarity : 0.005 0.051 1410 Dihedral : 6.964 95.137 1159 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.75 % Allowed : 12.16 % Favored : 84.09 % 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: 0.74 (0.26), residues: 1001 helix: 1.15 (0.25), residues: 414 sheet: 0.27 (0.33), residues: 224 loop : 0.05 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 99 HIS 0.009 0.002 HIS A 357 PHE 0.033 0.003 PHE N 108 TYR 0.024 0.002 TYR A 339 ARG 0.005 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 1.018 Fit side-chains REVERT: R 44 LEU cc_start: 0.6138 (OUTLIER) cc_final: 0.5414 (mm) REVERT: R 280 PHE cc_start: 0.7943 (t80) cc_final: 0.7595 (t80) REVERT: R 281 MET cc_start: 0.8779 (mmt) cc_final: 0.7822 (mmt) REVERT: B 59 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.8399 (t80) REVERT: B 197 ARG cc_start: 0.6944 (ttp80) cc_final: 0.6682 (ttp80) outliers start: 33 outliers final: 21 residues processed: 155 average time/residue: 0.2429 time to fit residues: 49.6208 Evaluate side-chains 150 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 76 HIS A 19 GLN A 23 ASN B 237 ASN B 239 ASN B 340 ASN N 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8213 Z= 0.206 Angle : 0.499 9.128 11120 Z= 0.271 Chirality : 0.041 0.186 1271 Planarity : 0.005 0.051 1410 Dihedral : 6.738 94.450 1159 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.30 % Allowed : 13.30 % Favored : 83.41 % 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: 0.93 (0.26), residues: 1001 helix: 1.31 (0.25), residues: 413 sheet: 0.32 (0.34), residues: 223 loop : 0.17 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.006 0.001 HIS A 357 PHE 0.017 0.002 PHE N 108 TYR 0.014 0.001 TYR A 339 ARG 0.003 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 0.954 Fit side-chains REVERT: R 44 LEU cc_start: 0.6126 (OUTLIER) cc_final: 0.5416 (mm) REVERT: R 280 PHE cc_start: 0.7915 (t80) cc_final: 0.7562 (t80) REVERT: R 281 MET cc_start: 0.8854 (mmt) cc_final: 0.7869 (mmt) REVERT: A 343 ASP cc_start: 0.7469 (m-30) cc_final: 0.6978 (m-30) REVERT: B 49 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7546 (mtt90) REVERT: B 59 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.8348 (t80) REVERT: B 197 ARG cc_start: 0.6855 (ttp80) cc_final: 0.6601 (ttp80) REVERT: B 226 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7442 (mt-10) REVERT: B 262 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8176 (ttm) outliers start: 29 outliers final: 20 residues processed: 150 average time/residue: 0.2183 time to fit residues: 43.7153 Evaluate side-chains 149 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 0.0370 chunk 86 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN B 340 ASN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8213 Z= 0.168 Angle : 0.475 8.989 11120 Z= 0.259 Chirality : 0.040 0.168 1271 Planarity : 0.004 0.051 1410 Dihedral : 6.554 91.948 1159 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.07 % Allowed : 13.41 % Favored : 83.52 % 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: 1.05 (0.26), residues: 1001 helix: 1.42 (0.25), residues: 413 sheet: 0.41 (0.35), residues: 217 loop : 0.21 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 339 HIS 0.005 0.001 HIS A 357 PHE 0.013 0.001 PHE R 262 TYR 0.013 0.001 TYR A 339 ARG 0.003 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 1.091 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.5988 (OUTLIER) cc_final: 0.5198 (mm) REVERT: R 280 PHE cc_start: 0.7874 (t80) cc_final: 0.7580 (t80) REVERT: R 281 MET cc_start: 0.8855 (mmt) cc_final: 0.7916 (mmt) REVERT: A 240 ASP cc_start: 0.8167 (p0) cc_final: 0.7676 (p0) REVERT: A 343 ASP cc_start: 0.7431 (m-30) cc_final: 0.6944 (m-30) REVERT: B 23 LYS cc_start: 0.8083 (tppt) cc_final: 0.7883 (tppt) REVERT: B 59 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.8329 (t80) REVERT: B 197 ARG cc_start: 0.6805 (ttp80) cc_final: 0.6562 (ttp80) REVERT: B 226 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7478 (mt-10) outliers start: 27 outliers final: 23 residues processed: 151 average time/residue: 0.2194 time to fit residues: 44.2753 Evaluate side-chains 156 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 80 optimal weight: 0.0470 chunk 84 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN B 88 ASN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8213 Z= 0.148 Angle : 0.461 8.937 11120 Z= 0.251 Chirality : 0.040 0.155 1271 Planarity : 0.004 0.051 1410 Dihedral : 6.409 89.005 1159 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.18 % Allowed : 13.41 % Favored : 83.41 % 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: 1.15 (0.27), residues: 1001 helix: 1.51 (0.25), residues: 413 sheet: 0.51 (0.35), residues: 223 loop : 0.21 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 339 HIS 0.004 0.001 HIS A 357 PHE 0.012 0.001 PHE A 222 TYR 0.012 0.001 TYR A 339 ARG 0.003 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.6012 (OUTLIER) cc_final: 0.5210 (mm) REVERT: R 280 PHE cc_start: 0.7890 (t80) cc_final: 0.7631 (t80) REVERT: R 281 MET cc_start: 0.8825 (mmt) cc_final: 0.7913 (mmt) REVERT: A 240 ASP cc_start: 0.8120 (p0) cc_final: 0.7638 (p0) REVERT: A 343 ASP cc_start: 0.7407 (m-30) cc_final: 0.6900 (m-30) REVERT: B 59 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.8309 (t80) REVERT: B 197 ARG cc_start: 0.6807 (ttp80) cc_final: 0.6579 (ttp80) REVERT: B 226 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7350 (mt-10) REVERT: G 47 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7315 (mt-10) outliers start: 28 outliers final: 26 residues processed: 152 average time/residue: 0.2195 time to fit residues: 44.8417 Evaluate side-chains 163 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8213 Z= 0.328 Angle : 0.565 9.284 11120 Z= 0.305 Chirality : 0.043 0.180 1271 Planarity : 0.005 0.050 1410 Dihedral : 6.743 91.635 1159 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.18 % Allowed : 13.41 % Favored : 83.41 % 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: 0.79 (0.26), residues: 1001 helix: 1.23 (0.25), residues: 413 sheet: 0.20 (0.33), residues: 232 loop : 0.10 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 339 HIS 0.008 0.002 HIS A 357 PHE 0.029 0.002 PHE N 108 TYR 0.020 0.002 TYR A 339 ARG 0.003 0.000 ARG B 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 0.961 Fit side-chains REVERT: R 44 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5295 (mm) REVERT: R 280 PHE cc_start: 0.7920 (t80) cc_final: 0.7653 (t80) REVERT: R 281 MET cc_start: 0.8905 (mmt) cc_final: 0.7937 (mmt) REVERT: A 343 ASP cc_start: 0.7491 (m-30) cc_final: 0.6991 (m-30) REVERT: B 59 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.8388 (t80) REVERT: B 226 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7572 (mt-10) REVERT: G 47 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7348 (mt-10) outliers start: 28 outliers final: 24 residues processed: 148 average time/residue: 0.2339 time to fit residues: 46.3163 Evaluate side-chains 158 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN B 340 ASN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.168893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.132640 restraints weight = 8688.889| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.69 r_work: 0.3301 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8213 Z= 0.165 Angle : 0.479 10.211 11120 Z= 0.259 Chirality : 0.040 0.171 1271 Planarity : 0.004 0.051 1410 Dihedral : 6.512 89.339 1159 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.07 % Allowed : 13.75 % Favored : 83.18 % 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: 1.02 (0.27), residues: 1001 helix: 1.48 (0.25), residues: 410 sheet: 0.35 (0.34), residues: 223 loop : 0.14 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 339 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE B 199 TYR 0.012 0.001 TYR A 339 ARG 0.003 0.000 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2162.93 seconds wall clock time: 39 minutes 52.92 seconds (2392.92 seconds total)