Starting phenix.real_space_refine on Fri Dec 8 12:24:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cz5_30505/12_2023/7cz5_30505_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cz5_30505/12_2023/7cz5_30505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cz5_30505/12_2023/7cz5_30505.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cz5_30505/12_2023/7cz5_30505.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cz5_30505/12_2023/7cz5_30505_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cz5_30505/12_2023/7cz5_30505_updated.pdb" } resolution = 2.6 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= 0.006 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 46 5.16 5 C 5304 2.51 5 N 1444 2.21 5 O 1542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 156": "NH1" <-> "NH2" Residue "R GLU 268": "OE1" <-> "OE2" Residue "R GLU 312": "OE1" <-> "OE2" Residue "R PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 357": "NH1" <-> "NH2" Residue "R GLU 386": "OE1" <-> "OE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "N PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8336 Number of models: 1 Model: "" Number of chains: 11 Chain: "R" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2155 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1893 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 3 Chain: "P" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 224 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} 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: {'CIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain: "R" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'CLR': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.77, per 1000 atoms: 0.57 Number of scatterers: 8336 At special positions: 0 Unit cell: (97.344, 97.344, 135.876, 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 46 16.00 O 1542 8.00 N 1444 7.00 C 5304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 202 " - pdb=" SG CYS R 272 " distance=2.02 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: 3.29 Conformation dependent library (CDL) restraints added in 1.5 seconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 10 sheets defined 36.7% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'R' and resid 120 through 153 Processing helix chain 'R' and resid 155 through 157 No H-bonds generated for 'chain 'R' and resid 155 through 157' Processing helix chain 'R' and resid 160 through 186 removed outlier: 3.834A pdb=" N VAL R 164 " --> pdb=" O PRO R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 232 Processing helix chain 'R' and resid 240 through 267 removed outlier: 3.760A pdb=" N TRP R 250 " --> pdb=" O VAL R 246 " (cutoff:3.500A) Proline residue: R 253 - end of helix removed outlier: 3.509A pdb=" N PHE R 267 " --> pdb=" O CYS R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 273 No H-bonds generated for 'chain 'R' and resid 271 through 273' Processing helix chain 'R' and resid 283 through 310 Proline residue: R 288 - end of helix removed outlier: 3.515A pdb=" N GLY R 298 " --> pdb=" O GLY R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 325 through 338 Proline residue: R 336 - end of helix Processing helix chain 'R' and resid 340 through 342 No H-bonds generated for 'chain 'R' and resid 340 through 342' Processing helix chain 'R' and resid 354 through 362 removed outlier: 3.698A pdb=" N LEU R 358 " --> pdb=" O LEU R 354 " (cutoff:3.500A) Proline residue: R 359 - end of helix Processing helix chain 'R' and resid 368 through 376 Processing helix chain 'R' and resid 381 through 392 removed outlier: 4.484A pdb=" N GLU R 386 " --> pdb=" O GLU R 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 38 removed outlier: 3.693A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 57 No H-bonds generated for 'chain 'A' and resid 54 through 57' Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 350 Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'P' and resid 3 through 27 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 7 through 21 removed outlier: 3.708A pdb=" N GLN G 11 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 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: 7.090A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.617A 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: 6.881A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.825A 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: 6.662A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.156A 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: 6.635A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.784A 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: 7.087A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.471A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.558A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.528A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (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 122 through 124 removed outlier: 6.267A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 371 hydrogen bonds defined for protein. 1038 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: 2.25 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2565 1.34 - 1.46: 2200 1.46 - 1.59: 3680 1.59 - 1.72: 0 1.72 - 1.84: 62 Bond restraints: 8507 Sorted by residual: bond pdb=" C1 PLM A 401 " pdb=" O1 PLM A 401 " ideal model delta sigma weight residual 1.249 1.342 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C1 PLM R 601 " pdb=" O1 PLM R 601 " ideal model delta sigma weight residual 1.249 1.342 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C1 PLM R 601 " pdb=" O2 PLM R 601 " ideal model delta sigma weight residual 1.249 1.208 0.041 2.00e-02 2.50e+03 4.19e+00 bond pdb=" C1 PLM A 401 " pdb=" O2 PLM A 401 " ideal model delta sigma weight residual 1.249 1.209 0.040 2.00e-02 2.50e+03 4.05e+00 bond pdb=" C1 PLM A 401 " pdb=" C2 PLM A 401 " ideal model delta sigma weight residual 1.542 1.505 0.037 2.00e-02 2.50e+03 3.38e+00 ... (remaining 8502 not shown) Histogram of bond angle deviations from ideal: 100.16 - 106.94: 178 106.94 - 113.72: 4771 113.72 - 120.50: 3348 120.50 - 127.29: 3125 127.29 - 134.07: 94 Bond angle restraints: 11516 Sorted by residual: angle pdb=" CA TYR R 133 " pdb=" CB TYR R 133 " pdb=" CG TYR R 133 " ideal model delta sigma weight residual 113.90 119.99 -6.09 1.80e+00 3.09e-01 1.14e+01 angle pdb=" C ILE R 132 " pdb=" N TYR R 133 " pdb=" CA TYR R 133 " ideal model delta sigma weight residual 121.14 115.26 5.88 1.75e+00 3.27e-01 1.13e+01 angle pdb=" N TYR R 226 " pdb=" CA TYR R 226 " pdb=" C TYR R 226 " ideal model delta sigma weight residual 111.28 114.82 -3.54 1.09e+00 8.42e-01 1.06e+01 angle pdb=" CA TRP B 99 " pdb=" CB TRP B 99 " pdb=" CG TRP B 99 " ideal model delta sigma weight residual 113.60 107.64 5.96 1.90e+00 2.77e-01 9.84e+00 angle pdb=" CA TRP R 219 " pdb=" CB TRP R 219 " pdb=" CG TRP R 219 " ideal model delta sigma weight residual 113.60 108.30 5.30 1.90e+00 2.77e-01 7.78e+00 ... (remaining 11511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 4651 17.38 - 34.76: 370 34.76 - 52.14: 49 52.14 - 69.52: 16 69.52 - 86.90: 6 Dihedral angle restraints: 5092 sinusoidal: 2059 harmonic: 3033 Sorted by residual: dihedral pdb=" CB CYS R 202 " pdb=" SG CYS R 202 " pdb=" SG CYS R 272 " pdb=" CB CYS R 272 " ideal model delta sinusoidal sigma weight residual 93.00 51.17 41.83 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" CA ILE R 270 " pdb=" C ILE R 270 " pdb=" N ALA R 271 " pdb=" CA ALA R 271 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 5089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1222 0.095 - 0.190: 66 0.190 - 0.285: 1 0.285 - 0.380: 1 0.380 - 0.475: 1 Chirality restraints: 1291 Sorted by residual: chirality pdb=" C14 CLR R 602 " pdb=" C13 CLR R 602 " pdb=" C15 CLR R 602 " pdb=" C8 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.32 -2.79 0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" C10 CLR R 602 " pdb=" C1 CLR R 602 " pdb=" C5 CLR R 602 " pdb=" C9 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.85 -2.52 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" C17 CLR R 602 " pdb=" C13 CLR R 602 " pdb=" C16 CLR R 602 " pdb=" C20 CLR R 602 " both_signs ideal model delta sigma weight residual False 2.55 2.81 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1288 not shown) Planarity restraints: 1459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 99 " -0.021 2.00e-02 2.50e+03 1.14e-02 3.27e+00 pdb=" CG TRP B 99 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP B 99 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP B 99 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 99 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 99 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 99 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 99 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 99 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 99 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO G 49 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 1 " 0.012 2.00e-02 2.50e+03 1.16e-02 2.69e+00 pdb=" CG TYR P 1 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR P 1 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR P 1 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR P 1 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR P 1 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR P 1 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR P 1 " -0.001 2.00e-02 2.50e+03 ... (remaining 1456 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 512 2.73 - 3.27: 8173 3.27 - 3.81: 13400 3.81 - 4.36: 17193 4.36 - 4.90: 29265 Nonbonded interactions: 68543 Sorted by model distance: nonbonded pdb=" O GLY N 8 " pdb=" OG1 THR N 122 " model vdw 2.186 2.440 nonbonded pdb=" OD1 ASN R 380 " pdb=" O HOH R 701 " model vdw 2.258 2.440 nonbonded pdb=" O GLY B 310 " pdb=" NZ LYS B 337 " model vdw 2.261 2.520 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.296 2.520 nonbonded pdb=" ND2 ASN R 380 " pdb=" OE2 GLU R 382 " model vdw 2.304 2.520 ... (remaining 68538 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: 0.670 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: 3.030 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.880 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 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 0.093 8507 Z= 0.285 Angle : 0.686 7.677 11516 Z= 0.368 Chirality : 0.049 0.475 1291 Planarity : 0.004 0.042 1459 Dihedral : 13.226 86.899 3125 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: -2.04 (0.24), residues: 1026 helix: -0.70 (0.24), residues: 413 sheet: -0.89 (0.32), residues: 218 loop : -2.23 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 99 HIS 0.014 0.001 HIS A 357 PHE 0.019 0.002 PHE B 151 TYR 0.027 0.002 TYR P 1 ARG 0.003 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.966 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 1.4261 time to fit residues: 205.0503 Evaluate side-chains 102 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.966 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 0.0970 chunk 90 optimal weight: 3.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 323 GLN A 14 ASN A 29 GLN A 267 GLN A 292 ASN P 8 ASN B 35 ASN B 91 HIS B 340 ASN G 18 GLN G 24 ASN N 3 GLN N 84 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8507 Z= 0.188 Angle : 0.562 9.272 11516 Z= 0.299 Chirality : 0.043 0.193 1291 Planarity : 0.004 0.042 1459 Dihedral : 6.758 53.324 1228 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.57 % Allowed : 9.19 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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 (0.25), residues: 1026 helix: 0.37 (0.26), residues: 412 sheet: -0.33 (0.34), residues: 207 loop : -1.77 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 219 HIS 0.008 0.001 HIS A 357 PHE 0.014 0.001 PHE B 199 TYR 0.035 0.001 TYR R 133 ARG 0.008 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 0.960 Fit side-chains outliers start: 14 outliers final: 3 residues processed: 120 average time/residue: 1.3153 time to fit residues: 167.3769 Evaluate side-chains 105 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 0.976 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 1.7413 time to fit residues: 3.1251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 75 optimal weight: 0.3980 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 35 ASN B 75 GLN B 266 HIS B 268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8507 Z= 0.152 Angle : 0.503 7.568 11516 Z= 0.269 Chirality : 0.042 0.173 1291 Planarity : 0.004 0.043 1459 Dihedral : 6.358 54.366 1228 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.46 % Allowed : 11.66 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: -0.40 (0.26), residues: 1026 helix: 0.89 (0.27), residues: 413 sheet: -0.33 (0.34), residues: 210 loop : -1.41 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 219 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.001 PHE B 199 TYR 0.029 0.001 TYR R 133 ARG 0.005 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 1.095 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 120 average time/residue: 1.2650 time to fit residues: 162.2789 Evaluate side-chains 106 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 0.984 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.2128 time to fit residues: 1.5196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 210 HIS A 59 GLN A 264 ASN A 292 ASN B 35 ASN B 75 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8507 Z= 0.288 Angle : 0.571 6.802 11516 Z= 0.307 Chirality : 0.045 0.173 1291 Planarity : 0.004 0.044 1459 Dihedral : 6.654 53.294 1228 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.69 % Allowed : 12.56 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: -0.33 (0.26), residues: 1026 helix: 0.80 (0.26), residues: 414 sheet: 0.04 (0.34), residues: 205 loop : -1.40 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 219 HIS 0.013 0.001 HIS A 357 PHE 0.022 0.002 PHE P 6 TYR 0.030 0.002 TYR R 133 ARG 0.003 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 1.107 Fit side-chains outliers start: 24 outliers final: 13 residues processed: 113 average time/residue: 1.2887 time to fit residues: 154.7846 Evaluate side-chains 110 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.937 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 4 average time/residue: 0.5684 time to fit residues: 3.8968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 82 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8507 Z= 0.297 Angle : 0.576 6.729 11516 Z= 0.309 Chirality : 0.045 0.171 1291 Planarity : 0.004 0.043 1459 Dihedral : 6.787 59.208 1228 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.58 % Allowed : 14.80 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: -0.32 (0.26), residues: 1026 helix: 0.78 (0.26), residues: 414 sheet: 0.12 (0.34), residues: 205 loop : -1.40 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 219 HIS 0.013 0.001 HIS A 357 PHE 0.018 0.002 PHE P 6 TYR 0.028 0.002 TYR R 133 ARG 0.006 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 0.904 Fit side-chains outliers start: 23 outliers final: 12 residues processed: 117 average time/residue: 1.3225 time to fit residues: 164.7953 Evaluate side-chains 108 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 1.078 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.2375 time to fit residues: 2.5885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.0980 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 0.0670 chunk 96 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 165 HIS A 264 ASN A 292 ASN B 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8507 Z= 0.129 Angle : 0.474 5.685 11516 Z= 0.255 Chirality : 0.041 0.166 1291 Planarity : 0.004 0.046 1459 Dihedral : 6.201 57.584 1228 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.91 % Allowed : 15.81 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.26), residues: 1026 helix: 1.25 (0.27), residues: 412 sheet: -0.06 (0.33), residues: 210 loop : -1.16 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 219 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.001 PHE P 6 TYR 0.023 0.001 TYR R 133 ARG 0.005 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 100 time to evaluate : 1.078 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 111 average time/residue: 1.3659 time to fit residues: 160.9339 Evaluate side-chains 100 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.985 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.2214 time to fit residues: 1.6196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 75 GLN N 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8507 Z= 0.356 Angle : 0.602 6.548 11516 Z= 0.323 Chirality : 0.046 0.169 1291 Planarity : 0.005 0.043 1459 Dihedral : 6.732 55.721 1228 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.24 % Allowed : 15.92 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: -0.17 (0.26), residues: 1026 helix: 0.90 (0.26), residues: 413 sheet: 0.18 (0.33), residues: 205 loop : -1.28 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 219 HIS 0.012 0.001 HIS A 357 PHE 0.020 0.002 PHE B 151 TYR 0.027 0.002 TYR R 133 ARG 0.006 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.987 Fit side-chains outliers start: 20 outliers final: 13 residues processed: 108 average time/residue: 1.3559 time to fit residues: 155.5325 Evaluate side-chains 105 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.7649 time to fit residues: 3.8650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 87 optimal weight: 0.0870 chunk 92 optimal weight: 3.9990 chunk 84 optimal weight: 0.0000 chunk 89 optimal weight: 2.9990 overall best weight: 0.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8507 Z= 0.140 Angle : 0.484 6.016 11516 Z= 0.260 Chirality : 0.041 0.168 1291 Planarity : 0.004 0.045 1459 Dihedral : 6.191 59.857 1228 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.79 % Allowed : 16.59 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 0.15 (0.26), residues: 1026 helix: 1.28 (0.27), residues: 412 sheet: 0.05 (0.33), residues: 208 loop : -1.08 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 219 HIS 0.006 0.001 HIS A 357 PHE 0.014 0.001 PHE P 6 TYR 0.022 0.001 TYR R 133 ARG 0.007 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 1.004 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 108 average time/residue: 1.4186 time to fit residues: 163.7826 Evaluate side-chains 104 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 1.042 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.2615 time to fit residues: 1.7226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 chunk 70 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 340 ASN N 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8507 Z= 0.200 Angle : 0.527 9.632 11516 Z= 0.279 Chirality : 0.042 0.169 1291 Planarity : 0.004 0.045 1459 Dihedral : 6.267 59.331 1228 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.02 % Allowed : 16.70 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 0.15 (0.26), residues: 1026 helix: 1.23 (0.27), residues: 413 sheet: 0.21 (0.33), residues: 205 loop : -1.11 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 219 HIS 0.007 0.001 HIS A 357 PHE 0.016 0.001 PHE A 212 TYR 0.024 0.001 TYR R 133 ARG 0.005 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 0.938 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 107 average time/residue: 1.3730 time to fit residues: 156.1424 Evaluate side-chains 103 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 1.042 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.1610 time to fit residues: 1.8795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN N 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8507 Z= 0.336 Angle : 0.603 9.501 11516 Z= 0.320 Chirality : 0.045 0.170 1291 Planarity : 0.004 0.043 1459 Dihedral : 6.562 58.612 1228 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.57 % Allowed : 16.93 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: -0.04 (0.26), residues: 1026 helix: 0.99 (0.26), residues: 413 sheet: 0.22 (0.34), residues: 205 loop : -1.17 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 219 HIS 0.014 0.002 HIS A 357 PHE 0.020 0.002 PHE A 212 TYR 0.029 0.002 TYR R 133 ARG 0.007 0.000 ARG A 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 1.039 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 104 average time/residue: 1.3580 time to fit residues: 149.9780 Evaluate side-chains 103 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 1.3259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.0270 chunk 79 optimal weight: 0.8980 chunk 33 optimal weight: 0.0970 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.178340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.134266 restraints weight = 9242.269| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.01 r_work: 0.3603 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8507 Z= 0.138 Angle : 0.487 5.851 11516 Z= 0.260 Chirality : 0.041 0.168 1291 Planarity : 0.004 0.044 1459 Dihedral : 6.001 57.030 1228 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.23 % Allowed : 17.38 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 0.26 (0.26), residues: 1026 helix: 1.34 (0.27), residues: 413 sheet: 0.11 (0.33), residues: 208 loop : -0.98 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 219 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.022 0.001 TYR R 133 ARG 0.007 0.000 ARG A 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3454.93 seconds wall clock time: 62 minutes 1.09 seconds (3721.09 seconds total)