Starting phenix.real_space_refine on Wed Feb 14 01:01:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xou_33359/02_2024/7xou_33359_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xou_33359/02_2024/7xou_33359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xou_33359/02_2024/7xou_33359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xou_33359/02_2024/7xou_33359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xou_33359/02_2024/7xou_33359_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xou_33359/02_2024/7xou_33359_updated.pdb" } resolution = 3.2 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: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5231 2.51 5 N 1433 2.21 5 O 1520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 38": "NH1" <-> "NH2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "R ARG 73": "NH1" <-> "NH2" Residue "R ARG 310": "NH1" <-> "NH2" Residue "R ARG 345": "NH1" <-> "NH2" 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: 8247 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'NH2': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1884 Classifications: {'peptide': 227} 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: 2288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2288 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 11, 'TRANS': 275} Chain breaks: 1 Time building chain proxies: 4.56, per 1000 atoms: 0.55 Number of scatterers: 8247 At special positions: 0 Unit cell: (90.246, 91.26, 129.792, 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 63 16.00 O 1520 8.00 N 1433 7.00 C 5231 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 196 " distance=2.04 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: 3.19 Conformation dependent library (CDL) restraints added in 1.2 seconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 11 sheets defined 36.5% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 13 through 37 removed outlier: 3.545A pdb=" N ILE A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.724A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 389 removed outlier: 4.499A pdb=" N ASN A 377 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN A 384 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ARG A 385 " --> pdb=" O ILE A 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'G' and resid 8 through 21 removed outlier: 5.196A pdb=" N ARG G 13 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 47 removed outlier: 3.817A pdb=" N ALA G 45 " --> pdb=" O CYS G 41 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) 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 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 44 through 68 removed outlier: 3.976A pdb=" N PHE R 52 " --> pdb=" O TYR R 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER R 55 " --> pdb=" O ILE R 51 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLY R 58 " --> pdb=" O LEU R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 93 removed outlier: 3.980A pdb=" N PHE R 79 " --> pdb=" O VAL R 75 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LEU R 80 " --> pdb=" O THR R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 104 Proline residue: R 101 - end of helix Processing helix chain 'R' and resid 111 through 143 removed outlier: 4.612A pdb=" N THR R 116 " --> pdb=" O ALA R 112 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR R 117 " --> pdb=" O VAL R 113 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL R 125 " --> pdb=" O MET R 121 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY R 141 " --> pdb=" O LEU R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 172 Processing helix chain 'R' and resid 203 through 217 Processing helix chain 'R' and resid 220 through 243 removed outlier: 4.003A pdb=" N GLU R 243 " --> pdb=" O GLY R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 338 Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 350 through 369 removed outlier: 4.044A pdb=" N SER R 359 " --> pdb=" O ILE R 355 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR R 361 " --> pdb=" O LEU R 357 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N SER R 362 " --> pdb=" O LEU R 358 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER R 363 " --> pdb=" O SER R 359 " (cutoff:3.500A) Proline residue: R 367 - end of helix Processing helix chain 'R' and resid 376 through 384 removed outlier: 3.853A pdb=" N ALA R 383 " --> pdb=" O LEU R 379 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 286 through 291 removed outlier: 3.670A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 61 removed outlier: 6.861A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.075A 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: 6.905A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.688A 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: 6.857A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.923A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.198A 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: 6.977A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.099A 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: 6.560A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 337 through 339 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 122 through 124 removed outlier: 5.618A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 179 through 182 removed outlier: 3.606A pdb=" N ARG R 197 " --> pdb=" O SER R 180 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 981 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: 2.31 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2681 1.34 - 1.46: 1989 1.46 - 1.58: 3647 1.58 - 1.70: 1 1.70 - 1.82: 92 Bond restraints: 8410 Sorted by residual: bond pdb=" O1 TYS L 2 " pdb=" S TYS L 2 " ideal model delta sigma weight residual 1.462 1.630 -0.168 2.00e-02 2.50e+03 7.07e+01 bond pdb=" OH TYS L 2 " pdb=" S TYS L 2 " ideal model delta sigma weight residual 1.679 1.531 0.148 2.00e-02 2.50e+03 5.48e+01 bond pdb=" N TRP L 5 " pdb=" CA TRP L 5 " ideal model delta sigma weight residual 1.458 1.432 0.027 1.08e-02 8.57e+03 6.04e+00 bond pdb=" C VAL R 183 " pdb=" N PRO R 184 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.19e+00 bond pdb=" C GLY L 4 " pdb=" N TRP L 5 " ideal model delta sigma weight residual 1.336 1.313 0.023 1.55e-02 4.16e+03 2.30e+00 ... (remaining 8405 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.59: 194 106.59 - 113.45: 4557 113.45 - 120.30: 3179 120.30 - 127.16: 3368 127.16 - 134.01: 83 Bond angle restraints: 11381 Sorted by residual: angle pdb=" N TRP L 5 " pdb=" CA TRP L 5 " pdb=" C TRP L 5 " ideal model delta sigma weight residual 112.30 105.02 7.28 1.36e+00 5.41e-01 2.87e+01 angle pdb=" C MET L 6 " pdb=" CA MET L 6 " pdb=" CB MET L 6 " ideal model delta sigma weight residual 116.54 110.40 6.14 1.15e+00 7.56e-01 2.85e+01 angle pdb=" CA MET L 6 " pdb=" C MET L 6 " pdb=" N ASP L 7 " ideal model delta sigma weight residual 119.52 115.50 4.02 7.90e-01 1.60e+00 2.58e+01 angle pdb=" N SER R 180 " pdb=" CA SER R 180 " pdb=" C SER R 180 " ideal model delta sigma weight residual 108.45 114.06 -5.61 1.26e+00 6.30e-01 1.98e+01 angle pdb=" N VAL R 183 " pdb=" CA VAL R 183 " pdb=" C VAL R 183 " ideal model delta sigma weight residual 108.88 116.53 -7.65 2.16e+00 2.14e-01 1.25e+01 ... (remaining 11376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 4464 16.06 - 32.12: 461 32.12 - 48.18: 83 48.18 - 64.24: 17 64.24 - 80.31: 7 Dihedral angle restraints: 5032 sinusoidal: 1998 harmonic: 3034 Sorted by residual: dihedral pdb=" CB CYS R 114 " pdb=" SG CYS R 114 " pdb=" SG CYS R 196 " pdb=" CB CYS R 196 " ideal model delta sinusoidal sigma weight residual 93.00 173.31 -80.31 1 1.00e+01 1.00e-02 7.98e+01 dihedral pdb=" CA LEU R 200 " pdb=" C LEU R 200 " pdb=" N PRO R 201 " pdb=" CA PRO R 201 " ideal model delta harmonic sigma weight residual 180.00 -147.78 -32.22 0 5.00e+00 4.00e-02 4.15e+01 dihedral pdb=" CA CYS R 94 " pdb=" C CYS R 94 " pdb=" N MET R 95 " pdb=" CA MET R 95 " ideal model delta harmonic sigma weight residual 180.00 -151.11 -28.89 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 5029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 795 0.035 - 0.069: 333 0.069 - 0.104: 118 0.104 - 0.139: 37 0.139 - 0.174: 4 Chirality restraints: 1287 Sorted by residual: chirality pdb=" CA THR R 350 " pdb=" N THR R 350 " pdb=" C THR R 350 " pdb=" CB THR R 350 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CA PRO R 201 " pdb=" N PRO R 201 " pdb=" C PRO R 201 " pdb=" CB PRO R 201 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CA THR R 174 " pdb=" N THR R 174 " pdb=" C THR R 174 " pdb=" CB THR R 174 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.01e-01 ... (remaining 1284 not shown) Planarity restraints: 1446 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET R 95 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" C MET R 95 " -0.035 2.00e-02 2.50e+03 pdb=" O MET R 95 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO R 96 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET L 3 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" C MET L 3 " 0.034 2.00e-02 2.50e+03 pdb=" O MET L 3 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY L 4 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 242 " 0.010 2.00e-02 2.50e+03 1.44e-02 3.63e+00 pdb=" CG PHE R 242 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE R 242 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE R 242 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE R 242 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 242 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE R 242 " -0.001 2.00e-02 2.50e+03 ... (remaining 1443 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 790 2.74 - 3.28: 8426 3.28 - 3.82: 13565 3.82 - 4.36: 16403 4.36 - 4.90: 28094 Nonbonded interactions: 67278 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.205 2.440 nonbonded pdb=" OD2 ASP B 247 " pdb=" NH2 ARG B 251 " model vdw 2.206 2.520 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.209 2.440 nonbonded pdb=" OE2 GLU A 230 " pdb=" NH1 ARG A 232 " model vdw 2.209 2.520 nonbonded pdb=" O ASP A 368 " pdb=" ND2 ASN A 371 " model vdw 2.221 2.520 ... (remaining 67273 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: 0.320 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: 0.000 Extract box with map and model: 1.950 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.780 Find NCS groups from input model: 0.240 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 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 0.168 8410 Z= 0.230 Angle : 0.707 9.794 11381 Z= 0.395 Chirality : 0.045 0.174 1287 Planarity : 0.005 0.047 1446 Dihedral : 13.469 76.468 3055 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.11 % Allowed : 3.45 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -3.52 (0.22), residues: 1021 helix: -1.72 (0.22), residues: 384 sheet: -2.12 (0.30), residues: 221 loop : -2.94 (0.25), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.033 0.002 PHE R 242 TYR 0.014 0.001 TYR B 59 ARG 0.005 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 LEU cc_start: 0.8099 (mp) cc_final: 0.7885 (mp) REVERT: B 155 ASN cc_start: 0.8405 (t0) cc_final: 0.7831 (t0) REVERT: N 72 ARG cc_start: 0.6911 (ptm160) cc_final: 0.5861 (ptp-170) REVERT: R 105 LYS cc_start: 0.4547 (mttm) cc_final: 0.4273 (mptt) REVERT: R 306 MET cc_start: 0.6633 (tpp) cc_final: 0.6323 (tpp) REVERT: R 309 LYS cc_start: 0.6598 (ttpp) cc_final: 0.6389 (ptmt) outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.2432 time to fit residues: 60.8515 Evaluate side-chains 152 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 42 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 0.3980 chunk 40 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN N 120 GLN R 102 ASN R 181 ASN R 194 ASN R 238 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8410 Z= 0.154 Angle : 0.568 7.877 11381 Z= 0.295 Chirality : 0.042 0.165 1287 Planarity : 0.004 0.048 1446 Dihedral : 4.884 39.982 1133 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.02 % Favored : 95.89 % Rotamer: Outliers : 1.33 % Allowed : 12.68 % Favored : 85.98 % 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 (0.25), residues: 1021 helix: -0.19 (0.27), residues: 387 sheet: -1.33 (0.33), residues: 225 loop : -2.36 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 5 HIS 0.002 0.001 HIS B 91 PHE 0.018 0.001 PHE R 242 TYR 0.025 0.001 TYR N 60 ARG 0.002 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 165 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 291 LEU cc_start: 0.7994 (mp) cc_final: 0.7753 (mp) REVERT: B 155 ASN cc_start: 0.8340 (t0) cc_final: 0.7730 (t0) REVERT: G 48 ASP cc_start: 0.7807 (t70) cc_final: 0.7384 (p0) REVERT: N 72 ARG cc_start: 0.6953 (ptm160) cc_final: 0.5964 (ptp-170) REVERT: R 105 LYS cc_start: 0.4480 (mttm) cc_final: 0.4176 (mptt) REVERT: R 326 TRP cc_start: 0.7149 (m100) cc_final: 0.6909 (m100) outliers start: 12 outliers final: 7 residues processed: 170 average time/residue: 0.2289 time to fit residues: 51.7319 Evaluate side-chains 160 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 153 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 340 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 76 optimal weight: 0.0060 chunk 62 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8410 Z= 0.162 Angle : 0.564 9.025 11381 Z= 0.294 Chirality : 0.042 0.158 1287 Planarity : 0.004 0.048 1446 Dihedral : 4.793 41.214 1133 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.56 % Allowed : 14.46 % Favored : 82.98 % 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: -1.47 (0.26), residues: 1021 helix: 0.25 (0.27), residues: 387 sheet: -1.04 (0.33), residues: 230 loop : -2.10 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 5 HIS 0.003 0.001 HIS B 91 PHE 0.019 0.002 PHE A 363 TYR 0.017 0.001 TYR N 60 ARG 0.002 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 155 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 LEU cc_start: 0.7882 (mp) cc_final: 0.7625 (mp) REVERT: B 86 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8156 (p) REVERT: G 48 ASP cc_start: 0.7799 (t70) cc_final: 0.7504 (p0) REVERT: N 5 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.6711 (mp10) REVERT: N 72 ARG cc_start: 0.6935 (ptm160) cc_final: 0.5995 (ptp-170) REVERT: R 105 LYS cc_start: 0.4532 (mttm) cc_final: 0.4233 (mptt) outliers start: 23 outliers final: 13 residues processed: 165 average time/residue: 0.2213 time to fit residues: 48.4530 Evaluate side-chains 161 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 146 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 102 ASN Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 340 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 8410 Z= 0.443 Angle : 0.787 9.693 11381 Z= 0.410 Chirality : 0.050 0.160 1287 Planarity : 0.006 0.063 1446 Dihedral : 5.876 50.518 1133 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.13 % Favored : 91.67 % Rotamer: Outliers : 3.78 % Allowed : 17.35 % Favored : 78.87 % 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: -2.18 (0.25), residues: 1021 helix: -0.42 (0.26), residues: 379 sheet: -1.41 (0.33), residues: 230 loop : -2.37 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP L 5 HIS 0.012 0.002 HIS B 91 PHE 0.038 0.003 PHE R 377 TYR 0.028 0.003 TYR B 105 ARG 0.004 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 150 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: B 105 TYR cc_start: 0.7876 (OUTLIER) cc_final: 0.7303 (t80) REVERT: R 54 LEU cc_start: 0.7009 (mp) cc_final: 0.6801 (mp) REVERT: R 95 MET cc_start: 0.4702 (mmm) cc_final: 0.4258 (mmm) REVERT: R 144 CYS cc_start: 0.6883 (t) cc_final: 0.6379 (m) REVERT: R 195 MET cc_start: 0.7390 (mtt) cc_final: 0.6992 (mtt) REVERT: R 199 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7415 (mm) outliers start: 34 outliers final: 22 residues processed: 170 average time/residue: 0.2165 time to fit residues: 49.7218 Evaluate side-chains 166 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 185 PHE Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 340 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 67 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8410 Z= 0.272 Angle : 0.668 7.178 11381 Z= 0.350 Chirality : 0.045 0.158 1287 Planarity : 0.005 0.060 1446 Dihedral : 5.453 46.765 1133 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.66 % Favored : 93.24 % Rotamer: Outliers : 3.78 % Allowed : 20.58 % Favored : 75.64 % 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: -1.76 (0.26), residues: 1021 helix: -0.11 (0.27), residues: 381 sheet: -1.13 (0.34), residues: 219 loop : -2.13 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 5 HIS 0.007 0.001 HIS B 91 PHE 0.022 0.002 PHE N 108 TYR 0.019 0.002 TYR B 105 ARG 0.002 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 146 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 344 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: B 105 TYR cc_start: 0.7683 (OUTLIER) cc_final: 0.7130 (t80) REVERT: G 48 ASP cc_start: 0.7875 (t70) cc_final: 0.7666 (p0) REVERT: R 95 MET cc_start: 0.4793 (mmm) cc_final: 0.3838 (mmm) REVERT: R 105 LYS cc_start: 0.4814 (mttm) cc_final: 0.4423 (mptt) REVERT: R 199 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7267 (mm) outliers start: 34 outliers final: 18 residues processed: 166 average time/residue: 0.2123 time to fit residues: 47.6824 Evaluate side-chains 161 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 140 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 340 THR Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 0.0570 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8410 Z= 0.161 Angle : 0.593 8.002 11381 Z= 0.310 Chirality : 0.042 0.156 1287 Planarity : 0.004 0.055 1446 Dihedral : 4.914 45.945 1133 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.70 % Favored : 95.20 % Rotamer: Outliers : 2.89 % Allowed : 22.02 % Favored : 75.08 % 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: -1.10 (0.26), residues: 1021 helix: 0.42 (0.27), residues: 384 sheet: -0.77 (0.34), residues: 224 loop : -1.75 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 209 HIS 0.003 0.001 HIS A 220 PHE 0.017 0.001 PHE R 198 TYR 0.015 0.001 TYR R 176 ARG 0.003 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: G 48 ASP cc_start: 0.7791 (t70) cc_final: 0.7536 (p0) REVERT: N 76 LYS cc_start: 0.7223 (mmtm) cc_final: 0.6775 (mmmt) REVERT: R 54 LEU cc_start: 0.7179 (tp) cc_final: 0.6931 (tt) REVERT: R 95 MET cc_start: 0.4344 (mmm) cc_final: 0.4018 (mmm) REVERT: R 105 LYS cc_start: 0.4696 (mttm) cc_final: 0.4329 (mptt) REVERT: R 199 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7137 (mm) REVERT: R 200 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7092 (mp) outliers start: 26 outliers final: 16 residues processed: 166 average time/residue: 0.2125 time to fit residues: 47.8336 Evaluate side-chains 160 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 318 ILE Chi-restraints excluded: chain R residue 340 THR Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 71 optimal weight: 0.0570 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 0.0670 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN N 120 GLN R 102 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8410 Z= 0.168 Angle : 0.592 7.812 11381 Z= 0.311 Chirality : 0.042 0.169 1287 Planarity : 0.004 0.054 1446 Dihedral : 4.854 45.174 1133 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.51 % Favored : 95.40 % Rotamer: Outliers : 2.56 % Allowed : 22.91 % Favored : 74.53 % 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: 1021 helix: 0.56 (0.27), residues: 383 sheet: -0.59 (0.34), residues: 218 loop : -1.64 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 209 HIS 0.002 0.001 HIS B 91 PHE 0.023 0.001 PHE R 198 TYR 0.018 0.001 TYR N 60 ARG 0.003 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: G 48 ASP cc_start: 0.7765 (t70) cc_final: 0.7525 (p0) REVERT: N 76 LYS cc_start: 0.7180 (mmtm) cc_final: 0.6796 (mmmt) REVERT: R 95 MET cc_start: 0.4543 (mmm) cc_final: 0.4251 (mmm) REVERT: R 105 LYS cc_start: 0.4693 (mttm) cc_final: 0.4315 (mptt) REVERT: R 199 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7100 (mm) outliers start: 23 outliers final: 18 residues processed: 154 average time/residue: 0.2264 time to fit residues: 46.6595 Evaluate side-chains 152 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 102 ASN Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 318 ILE Chi-restraints excluded: chain R residue 340 THR Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 0.0870 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 340 ASN N 120 GLN R 102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8410 Z= 0.179 Angle : 0.592 7.754 11381 Z= 0.311 Chirality : 0.042 0.170 1287 Planarity : 0.004 0.047 1446 Dihedral : 4.756 44.576 1133 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.21 % Favored : 95.69 % Rotamer: Outliers : 2.89 % Allowed : 23.14 % Favored : 73.97 % 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: -0.75 (0.26), residues: 1021 helix: 0.69 (0.28), residues: 379 sheet: -0.46 (0.34), residues: 218 loop : -1.59 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 339 HIS 0.003 0.001 HIS B 91 PHE 0.027 0.001 PHE R 198 TYR 0.014 0.001 TYR R 176 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: G 48 ASP cc_start: 0.7721 (t70) cc_final: 0.7386 (p0) REVERT: N 76 LYS cc_start: 0.7164 (mmtm) cc_final: 0.6811 (mmmt) REVERT: R 95 MET cc_start: 0.4607 (mmm) cc_final: 0.4297 (mmm) REVERT: R 105 LYS cc_start: 0.4570 (mttm) cc_final: 0.4214 (mptt) REVERT: R 199 LEU cc_start: 0.7643 (mm) cc_final: 0.7085 (mm) outliers start: 26 outliers final: 19 residues processed: 155 average time/residue: 0.2236 time to fit residues: 46.7181 Evaluate side-chains 153 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 102 ASN Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 312 ILE Chi-restraints excluded: chain R residue 318 ILE Chi-restraints excluded: chain R residue 340 THR Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 54 optimal weight: 0.0570 chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6459 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8410 Z= 0.172 Angle : 0.598 8.148 11381 Z= 0.311 Chirality : 0.042 0.173 1287 Planarity : 0.004 0.043 1446 Dihedral : 4.675 43.700 1133 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.31 % Favored : 95.59 % Rotamer: Outliers : 2.22 % Allowed : 24.03 % Favored : 73.75 % 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: -0.69 (0.26), residues: 1021 helix: 0.70 (0.27), residues: 382 sheet: -0.36 (0.34), residues: 218 loop : -1.57 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 339 HIS 0.002 0.001 HIS B 91 PHE 0.028 0.001 PHE R 198 TYR 0.016 0.001 TYR N 60 ARG 0.005 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: G 48 ASP cc_start: 0.7697 (t70) cc_final: 0.7332 (p0) REVERT: R 95 MET cc_start: 0.4606 (mmm) cc_final: 0.4329 (mmm) REVERT: R 105 LYS cc_start: 0.4858 (mttm) cc_final: 0.4416 (mptt) REVERT: R 150 ARG cc_start: 0.6876 (OUTLIER) cc_final: 0.6305 (mtt180) REVERT: R 199 LEU cc_start: 0.7556 (mm) cc_final: 0.6971 (mm) outliers start: 20 outliers final: 16 residues processed: 148 average time/residue: 0.2297 time to fit residues: 45.4021 Evaluate side-chains 151 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 312 ILE Chi-restraints excluded: chain R residue 318 ILE Chi-restraints excluded: chain R residue 340 THR Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 340 ASN R 102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8410 Z= 0.242 Angle : 0.644 7.997 11381 Z= 0.336 Chirality : 0.044 0.149 1287 Planarity : 0.005 0.044 1446 Dihedral : 4.936 45.443 1133 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.48 % Favored : 94.42 % Rotamer: Outliers : 2.67 % Allowed : 24.25 % Favored : 73.08 % 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: -0.92 (0.26), residues: 1021 helix: 0.43 (0.27), residues: 383 sheet: -0.47 (0.34), residues: 218 loop : -1.62 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 5 HIS 0.005 0.001 HIS B 91 PHE 0.029 0.002 PHE R 198 TYR 0.016 0.002 TYR B 105 ARG 0.005 0.000 ARG A 385 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: B 105 TYR cc_start: 0.7641 (OUTLIER) cc_final: 0.7171 (t80) REVERT: G 48 ASP cc_start: 0.7741 (t70) cc_final: 0.7378 (p0) REVERT: N 76 LYS cc_start: 0.7239 (mmtm) cc_final: 0.6774 (mmmt) REVERT: R 105 LYS cc_start: 0.4734 (mttm) cc_final: 0.4343 (mptt) REVERT: R 199 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7319 (mm) outliers start: 24 outliers final: 19 residues processed: 145 average time/residue: 0.2245 time to fit residues: 44.1653 Evaluate side-chains 154 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 102 ASN Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 312 ILE Chi-restraints excluded: chain R residue 318 ILE Chi-restraints excluded: chain R residue 340 THR Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN R 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.239516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.205741 restraints weight = 9003.008| |-----------------------------------------------------------------------------| r_work (start): 0.4515 rms_B_bonded: 2.55 r_work: 0.4366 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8410 Z= 0.236 Angle : 0.640 8.042 11381 Z= 0.334 Chirality : 0.043 0.152 1287 Planarity : 0.004 0.044 1446 Dihedral : 4.948 45.398 1133 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.39 % Favored : 94.52 % Rotamer: Outliers : 2.45 % Allowed : 24.47 % Favored : 73.08 % 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: -0.98 (0.26), residues: 1021 helix: 0.36 (0.27), residues: 383 sheet: -0.52 (0.34), residues: 218 loop : -1.63 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 5 HIS 0.005 0.001 HIS B 91 PHE 0.029 0.002 PHE R 198 TYR 0.016 0.001 TYR R 119 ARG 0.004 0.000 ARG A 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2016.60 seconds wall clock time: 37 minutes 24.80 seconds (2244.80 seconds total)