Starting phenix.real_space_refine on Tue Nov 14 19:22:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ha0_34585/11_2023/8ha0_34585_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ha0_34585/11_2023/8ha0_34585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ha0_34585/11_2023/8ha0_34585.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ha0_34585/11_2023/8ha0_34585.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ha0_34585/11_2023/8ha0_34585_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ha0_34585/11_2023/8ha0_34585_neut_updated.pdb" } resolution = 2.62 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= 0.002 sd= 0.026 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 60 5.16 5 C 6013 2.51 5 N 1616 2.21 5 O 1696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "R GLU 35": "OE1" <-> "OE2" Residue "R GLU 36": "OE1" <-> "OE2" Residue "R ARG 43": "NH1" <-> "NH2" Residue "R GLU 111": "OE1" <-> "OE2" Residue "R GLU 125": "OE1" <-> "OE2" Residue "R GLU 182": "OE1" <-> "OE2" Residue "R GLU 302": "OE1" <-> "OE2" Residue "R PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 317": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 9385 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1950 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2614 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 2 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: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "P" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 289 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "R" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 3113 Unusual residues: {'CLR': 4, 'PLM': 3} Classifications: {'peptide': 359, 'undetermined': 7} Link IDs: {'PTRANS': 11, 'TRANS': 347, None: 7} Not linked: pdbres="LEU R 481 " pdbres="CLR R1501 " Not linked: pdbres="CLR R1501 " pdbres="CLR R1502 " Not linked: pdbres="CLR R1502 " pdbres="CLR R1503 " Not linked: pdbres="CLR R1503 " pdbres="CLR R1504 " Not linked: pdbres="CLR R1504 " pdbres="PLM R1505 " ... (remaining 2 not shown) Chain breaks: 4 Time building chain proxies: 5.01, per 1000 atoms: 0.53 Number of scatterers: 9385 At special positions: 0 Unit cell: (159.856, 114.536, 102.176, 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 60 16.00 O 1696 8.00 N 1616 7.00 C 6013 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.08 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.06 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.6 seconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 12 sheets defined 38.4% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 56 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 253 through 277 removed outlier: 4.229A pdb=" N GLN A 267 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 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 349 removed outlier: 3.617A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 3.916A pdb=" N ALA A 372 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 3.826A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 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 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'P' and resid 3 through 33 removed outlier: 4.128A pdb=" N ASN P 33 " --> pdb=" O GLN P 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 47 Processing helix chain 'R' and resid 178 through 211 Processing helix chain 'R' and resid 218 through 244 Processing helix chain 'R' and resid 279 through 310 removed outlier: 3.580A pdb=" N GLY R 303 " --> pdb=" O ILE R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 321 through 346 removed outlier: 4.142A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 357 through 391 removed outlier: 4.221A pdb=" N LYS R 360 " --> pdb=" O GLY R 357 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N VAL R 365 " --> pdb=" O ILE R 362 " (cutoff:3.500A) Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 400 through 417 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 419 through 422 Processing helix chain 'R' and resid 435 through 460 removed outlier: 4.109A pdb=" N SER R 449 " --> pdb=" O MET R 445 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 464 through 480 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.404A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA A 243 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL A 224 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.933A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.356A 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: 6.806A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.669A 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: 6.924A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.205A 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: 7.057A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.400A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.390A 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: 5.007A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.102A 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: 6.395A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 45 through 51 removed outlier: 7.039A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.536A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.731A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 92 through 98 removed outlier: 3.630A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'R' and resid 128 through 130 430 hydrogen bonds defined for protein. 1119 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: 2.45 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 3009 1.34 - 1.49: 2470 1.49 - 1.63: 4035 1.63 - 1.77: 0 1.77 - 1.92: 86 Bond restraints: 9600 Sorted by residual: bond pdb=" N ASP R 149 " pdb=" CA ASP R 149 " ideal model delta sigma weight residual 1.457 1.559 -0.102 1.29e-02 6.01e+03 6.21e+01 bond pdb=" CA MET R 312 " pdb=" C MET R 312 " ideal model delta sigma weight residual 1.522 1.414 0.108 1.43e-02 4.89e+03 5.69e+01 bond pdb=" CA CYS R 148 " pdb=" CB CYS R 148 " ideal model delta sigma weight residual 1.524 1.620 -0.095 1.30e-02 5.92e+03 5.38e+01 bond pdb=" CA CYS R 148 " pdb=" C CYS R 148 " ideal model delta sigma weight residual 1.530 1.607 -0.076 1.14e-02 7.69e+03 4.50e+01 bond pdb=" N ALA R 313 " pdb=" CA ALA R 313 " ideal model delta sigma weight residual 1.457 1.374 0.084 1.29e-02 6.01e+03 4.19e+01 ... (remaining 9595 not shown) Histogram of bond angle deviations from ideal: 88.29 - 97.43: 2 97.43 - 106.58: 231 106.58 - 115.73: 5998 115.73 - 124.88: 6585 124.88 - 134.03: 186 Bond angle restraints: 13002 Sorted by residual: angle pdb=" N TYR R 320 " pdb=" CA TYR R 320 " pdb=" C TYR R 320 " ideal model delta sigma weight residual 112.30 88.29 24.01 1.36e+00 5.41e-01 3.12e+02 angle pdb=" N LYS R 318 " pdb=" CA LYS R 318 " pdb=" C LYS R 318 " ideal model delta sigma weight residual 113.02 100.05 12.97 1.49e+00 4.50e-01 7.58e+01 angle pdb=" N CYS R 148 " pdb=" CA CYS R 148 " pdb=" C CYS R 148 " ideal model delta sigma weight residual 110.68 99.56 11.12 1.39e+00 5.18e-01 6.40e+01 angle pdb=" C TYR R 320 " pdb=" N LEU R 321 " pdb=" CA LEU R 321 " ideal model delta sigma weight residual 120.54 130.92 -10.38 1.35e+00 5.49e-01 5.91e+01 angle pdb=" N ALA R 313 " pdb=" CA ALA R 313 " pdb=" C ALA R 313 " ideal model delta sigma weight residual 110.80 94.83 15.97 2.13e+00 2.20e-01 5.62e+01 ... (remaining 12997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 5169 17.52 - 35.03: 339 35.03 - 52.55: 104 52.55 - 70.06: 38 70.06 - 87.58: 6 Dihedral angle restraints: 5656 sinusoidal: 2295 harmonic: 3361 Sorted by residual: dihedral pdb=" CB CYS R 108 " pdb=" SG CYS R 108 " pdb=" SG CYS R 148 " pdb=" CB CYS R 148 " ideal model delta sinusoidal sigma weight residual 93.00 142.85 -49.85 1 1.00e+01 1.00e-02 3.41e+01 dihedral pdb=" CB CYS R 48 " pdb=" SG CYS R 48 " pdb=" SG CYS R 117 " pdb=" CB CYS R 117 " ideal model delta sinusoidal sigma weight residual 93.00 134.90 -41.90 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" N TYR R 320 " pdb=" C TYR R 320 " pdb=" CA TYR R 320 " pdb=" CB TYR R 320 " ideal model delta harmonic sigma weight residual 122.80 111.03 11.77 0 2.50e+00 1.60e-01 2.21e+01 ... (remaining 5653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1348 0.097 - 0.195: 71 0.195 - 0.292: 10 0.292 - 0.389: 6 0.389 - 0.487: 3 Chirality restraints: 1438 Sorted by residual: chirality pdb=" CA LEU R 116 " pdb=" N LEU R 116 " pdb=" C LEU R 116 " pdb=" CB LEU R 116 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" CA CYS R 460 " pdb=" N CYS R 460 " pdb=" C CYS R 460 " pdb=" CB CYS R 460 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CA LEU R 120 " pdb=" N LEU R 120 " pdb=" C LEU R 120 " pdb=" CB LEU R 120 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.69e+00 ... (remaining 1435 not shown) Planarity restraints: 1626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 311 " -0.054 2.00e-02 2.50e+03 1.07e-01 1.14e+02 pdb=" C PHE R 311 " 0.184 2.00e-02 2.50e+03 pdb=" O PHE R 311 " -0.072 2.00e-02 2.50e+03 pdb=" N MET R 312 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS R 114 " -0.029 2.00e-02 2.50e+03 5.80e-02 3.36e+01 pdb=" C HIS R 114 " 0.100 2.00e-02 2.50e+03 pdb=" O HIS R 114 " -0.038 2.00e-02 2.50e+03 pdb=" N ILE R 115 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 109 " 0.078 5.00e-02 4.00e+02 1.17e-01 2.21e+01 pdb=" N PRO R 110 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO R 110 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO R 110 " 0.060 5.00e-02 4.00e+02 ... (remaining 1623 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 19 2.33 - 2.97: 4733 2.97 - 3.62: 13822 3.62 - 4.26: 21937 4.26 - 4.90: 36833 Nonbonded interactions: 77344 Sorted by model distance: nonbonded pdb=" O PRO R 110 " pdb=" CZ3 TRP R 154 " model vdw 1.689 3.340 nonbonded pdb=" O PRO R 110 " pdb=" CH2 TRP R 154 " model vdw 1.747 3.340 nonbonded pdb=" SD MET R 189 " pdb=" C2 CLR R1504 " model vdw 1.936 3.040 nonbonded pdb=" N TYR R 320 " pdb=" N LEU R 321 " model vdw 2.091 2.560 nonbonded pdb=" C LYS R 50 " pdb=" CD LYS R 50 " model vdw 2.097 3.670 ... (remaining 77339 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: 1.610 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: 5.970 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 26.340 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: 0.000 Load rotamer database and sin/cos tables:10.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 9600 Z= 0.326 Angle : 0.783 24.015 13002 Z= 0.488 Chirality : 0.053 0.487 1438 Planarity : 0.005 0.117 1626 Dihedral : 13.825 87.580 3472 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.62 % Allowed : 2.21 % Favored : 97.18 % Rotamer: Outliers : 4.53 % Allowed : 5.14 % Favored : 90.33 % Cbeta Deviations : 0.18 % 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: -0.68 (0.24), residues: 1133 helix: 0.83 (0.24), residues: 455 sheet: -0.57 (0.31), residues: 216 loop : -1.69 (0.28), residues: 462 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 239 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 22 residues processed: 280 average time/residue: 1.2394 time to fit residues: 369.2489 Evaluate side-chains 215 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 193 time to evaluate : 0.933 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 2 average time/residue: 0.6283 time to fit residues: 2.7156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 13 GLN B 36 ASN B 268 ASN B 311 HIS P 6 GLN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 151 ASN R 161 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 9600 Z= 0.293 Angle : 0.618 8.494 13002 Z= 0.325 Chirality : 0.043 0.176 1438 Planarity : 0.006 0.095 1626 Dihedral : 7.115 56.157 1344 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.09 % Favored : 96.56 % Rotamer: Outliers : 4.83 % Allowed : 13.80 % Favored : 81.37 % 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: 0.35 (0.25), residues: 1133 helix: 1.73 (0.24), residues: 450 sheet: 0.03 (0.33), residues: 213 loop : -1.17 (0.28), residues: 470 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 180 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 33 residues processed: 219 average time/residue: 1.2328 time to fit residues: 288.2511 Evaluate side-chains 209 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 176 time to evaluate : 0.933 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 27 residues processed: 7 average time/residue: 0.4326 time to fit residues: 5.0038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 111 optimal weight: 0.0070 chunk 91 optimal weight: 0.5980 chunk 101 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 236 GLN R 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 9600 Z= 0.186 Angle : 0.517 6.943 13002 Z= 0.275 Chirality : 0.040 0.161 1438 Planarity : 0.005 0.098 1626 Dihedral : 6.474 56.802 1344 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.65 % Favored : 97.00 % Rotamer: Outliers : 5.54 % Allowed : 15.41 % Favored : 79.05 % 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: 0.77 (0.25), residues: 1133 helix: 2.14 (0.25), residues: 448 sheet: 0.34 (0.33), residues: 206 loop : -1.02 (0.28), residues: 479 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 180 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 29 residues processed: 220 average time/residue: 1.4589 time to fit residues: 339.6676 Evaluate side-chains 208 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 179 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 22 residues processed: 7 average time/residue: 0.1298 time to fit residues: 2.8155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 49 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 236 GLN B 88 ASN B 220 GLN R 37 GLN R 143 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 9600 Z= 0.231 Angle : 0.535 7.508 13002 Z= 0.283 Chirality : 0.041 0.169 1438 Planarity : 0.005 0.095 1626 Dihedral : 6.218 55.824 1344 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.00 % Favored : 96.65 % Rotamer: Outliers : 5.24 % Allowed : 16.62 % Favored : 78.15 % 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: 0.86 (0.25), residues: 1133 helix: 2.19 (0.25), residues: 448 sheet: 0.31 (0.33), residues: 211 loop : -0.91 (0.28), residues: 474 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 169 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 39 residues processed: 203 average time/residue: 1.5132 time to fit residues: 324.7898 Evaluate side-chains 208 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 169 time to evaluate : 0.989 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 28 residues processed: 12 average time/residue: 0.5620 time to fit residues: 9.0478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.0980 chunk 1 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 A 236 GLN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 9600 Z= 0.295 Angle : 0.555 7.877 13002 Z= 0.295 Chirality : 0.042 0.179 1438 Planarity : 0.005 0.096 1626 Dihedral : 6.227 55.594 1344 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.18 % Favored : 96.47 % Rotamer: Outliers : 5.24 % Allowed : 16.62 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.25), residues: 1133 helix: 2.10 (0.25), residues: 449 sheet: 0.50 (0.33), residues: 209 loop : -0.89 (0.27), residues: 475 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 163 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 39 residues processed: 196 average time/residue: 1.5163 time to fit residues: 313.9631 Evaluate side-chains 200 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 161 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 29 residues processed: 11 average time/residue: 0.7089 time to fit residues: 10.0208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 26 optimal weight: 0.1980 chunk 109 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 105 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 236 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 9600 Z= 0.195 Angle : 0.505 7.394 13002 Z= 0.269 Chirality : 0.040 0.168 1438 Planarity : 0.005 0.096 1626 Dihedral : 6.002 56.743 1344 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.74 % Favored : 96.91 % Rotamer: Outliers : 4.33 % Allowed : 17.62 % Favored : 78.05 % 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: 1.04 (0.25), residues: 1133 helix: 2.24 (0.25), residues: 446 sheet: 0.57 (0.33), residues: 209 loop : -0.77 (0.28), residues: 478 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 171 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 30 residues processed: 204 average time/residue: 1.5670 time to fit residues: 337.4141 Evaluate side-chains 197 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 167 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 27 residues processed: 4 average time/residue: 0.6275 time to fit residues: 4.3231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 0.1980 chunk 50 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 218 ASN A 220 HIS A 236 GLN N 77 ASN R 220 ASN R 358 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 9600 Z= 0.246 Angle : 0.536 7.656 13002 Z= 0.284 Chirality : 0.041 0.176 1438 Planarity : 0.005 0.097 1626 Dihedral : 6.023 58.163 1344 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.18 % Favored : 96.47 % Rotamer: Outliers : 4.43 % Allowed : 17.42 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.25), residues: 1133 helix: 2.13 (0.25), residues: 449 sheet: 0.54 (0.33), residues: 211 loop : -0.85 (0.28), residues: 473 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 170 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 36 residues processed: 203 average time/residue: 1.4521 time to fit residues: 311.7556 Evaluate side-chains 200 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 164 time to evaluate : 0.994 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 29 residues processed: 8 average time/residue: 0.5420 time to fit residues: 6.3070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 220 HIS A 236 GLN B 239 ASN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 9600 Z= 0.262 Angle : 0.546 8.663 13002 Z= 0.288 Chirality : 0.042 0.176 1438 Planarity : 0.005 0.097 1626 Dihedral : 5.991 59.505 1344 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.09 % Favored : 96.56 % Rotamer: Outliers : 4.33 % Allowed : 17.22 % Favored : 78.45 % 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 (0.25), residues: 1133 helix: 2.09 (0.25), residues: 449 sheet: 0.51 (0.33), residues: 212 loop : -0.86 (0.28), residues: 472 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 162 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 33 residues processed: 194 average time/residue: 1.4512 time to fit residues: 298.1958 Evaluate side-chains 192 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 159 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 28 residues processed: 6 average time/residue: 0.3366 time to fit residues: 3.9205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.6980 chunk 104 optimal weight: 0.3980 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 79 optimal weight: 0.0030 chunk 31 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 220 HIS A 236 GLN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 9600 Z= 0.201 Angle : 0.524 6.837 13002 Z= 0.279 Chirality : 0.040 0.174 1438 Planarity : 0.006 0.098 1626 Dihedral : 5.841 59.672 1344 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.91 % Favored : 96.73 % Rotamer: Outliers : 3.63 % Allowed : 18.93 % Favored : 77.44 % 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: 1.01 (0.25), residues: 1133 helix: 2.16 (0.25), residues: 452 sheet: 0.55 (0.34), residues: 208 loop : -0.76 (0.28), residues: 473 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 159 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 34 residues processed: 189 average time/residue: 1.4460 time to fit residues: 289.5193 Evaluate side-chains 190 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 156 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 29 residues processed: 6 average time/residue: 0.6937 time to fit residues: 6.1035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.7980 chunk 74 optimal weight: 0.0970 chunk 112 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 69 optimal weight: 0.0570 chunk 54 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 220 HIS A 236 GLN N 77 ASN ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 9600 Z= 0.181 Angle : 0.514 6.573 13002 Z= 0.275 Chirality : 0.040 0.174 1438 Planarity : 0.006 0.099 1626 Dihedral : 5.723 58.838 1344 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.00 % Favored : 96.65 % Rotamer: Outliers : 3.12 % Allowed : 19.54 % Favored : 77.34 % 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: 1.06 (0.25), residues: 1133 helix: 2.24 (0.25), residues: 449 sheet: 0.57 (0.34), residues: 208 loop : -0.75 (0.28), residues: 476 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 163 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 29 residues processed: 190 average time/residue: 1.4345 time to fit residues: 288.9855 Evaluate side-chains 186 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 157 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 27 residues processed: 2 average time/residue: 1.1168 time to fit residues: 3.8414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 220 HIS A 236 GLN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.139567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.114616 restraints weight = 12745.837| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.66 r_work: 0.3397 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 9600 Z= 0.293 Angle : 0.561 7.501 13002 Z= 0.299 Chirality : 0.043 0.180 1438 Planarity : 0.006 0.099 1626 Dihedral : 5.871 58.735 1344 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.35 % Favored : 96.29 % Rotamer: Outliers : 2.82 % Allowed : 19.94 % Favored : 77.24 % 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 (0.25), residues: 1133 helix: 2.12 (0.25), residues: 449 sheet: 0.57 (0.34), residues: 209 loop : -0.75 (0.28), residues: 475 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5179.56 seconds wall clock time: 91 minutes 57.80 seconds (5517.80 seconds total)