Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 12:08:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duq_30866/04_2023/7duq_30866_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duq_30866/04_2023/7duq_30866.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duq_30866/04_2023/7duq_30866_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duq_30866/04_2023/7duq_30866_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duq_30866/04_2023/7duq_30866_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duq_30866/04_2023/7duq_30866.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duq_30866/04_2023/7duq_30866.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duq_30866/04_2023/7duq_30866_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duq_30866/04_2023/7duq_30866_trim_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.008 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: 5 Type Number sf(0) Gaussians S 55 5.16 5 Cl 2 4.86 5 C 6175 2.51 5 N 1632 2.21 5 O 1738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P GLU 27": "OE1" <-> "OE2" Residue "P ARG 36": "NH1" <-> "NH2" Residue "R GLU 138": "OE1" <-> "OE2" Residue "R GLU 262": "OE1" <-> "OE2" Residue "R ARG 310": "NH1" <-> "NH2" Residue "R GLU 408": "OE1" <-> "OE2" Residue "R ARG 414": "NH1" <-> "NH2" Residue "A ARG 13": "NH1" <-> "NH2" Residue "A GLU 16": "OE1" <-> "OE2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9602 Number of models: 1 Model: "" Number of chains: 7 Chain: "P" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "R" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3176 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 14, 'TRANS': 369} Chain breaks: 2 Chain: "A" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1990 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 2 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: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 213 Unusual residues: {'CLR': 7, 'HNO': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 5.53, per 1000 atoms: 0.58 Number of scatterers: 9602 At special positions: 0 Unit cell: (164.065, 105.545, 97.185, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 55 16.00 O 1738 8.00 N 1632 7.00 C 6175 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.04 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.26 Conformation dependent library (CDL) restraints added in 1.4 seconds 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2212 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 11 sheets defined 39.2% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'P' and resid 8 through 34 Processing helix chain 'R' and resid 32 through 52 Processing helix chain 'R' and resid 93 through 95 No H-bonds generated for 'chain 'R' and resid 93 through 95' Processing helix chain 'R' and resid 137 through 168 removed outlier: 4.531A pdb=" N LEU R 142 " --> pdb=" O GLU R 139 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR R 148 " --> pdb=" O TYR R 145 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL R 150 " --> pdb=" O ILE R 147 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE R 156 " --> pdb=" O ALA R 153 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU R 167 " --> pdb=" O ALA R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 172 No H-bonds generated for 'chain 'R' and resid 170 through 172' Processing helix chain 'R' and resid 175 through 204 Processing helix chain 'R' and resid 207 through 214 Processing helix chain 'R' and resid 224 through 255 removed outlier: 3.843A pdb=" N PHE R 230 " --> pdb=" O CYS R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 274 Processing helix chain 'R' and resid 276 through 291 removed outlier: 4.216A pdb=" N VAL R 281 " --> pdb=" O LEU R 278 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N VAL R 282 " --> pdb=" O LEU R 279 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 303 through 337 removed outlier: 3.692A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 360 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 365 Processing helix chain 'R' and resid 377 through 392 Processing helix chain 'R' and resid 394 through 402 Processing helix chain 'R' and resid 407 through 422 Processing helix chain 'A' and resid 12 through 38 Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 53 through 62 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 294 through 302 removed outlier: 4.100A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) 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 350 Processing helix chain 'A' and resid 369 through 390 removed outlier: 4.271A pdb=" N VAL A 375 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.978A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.686A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 30 through 43 removed outlier: 3.570A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 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 'R' and resid 80 through 84 Processing sheet with id= B, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.215A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.792A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.932A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.539A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.911A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.631A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.371A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.612A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.746A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 439 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: 2.81 Time building geometry restraints manager: 4.48 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: 3039 1.34 - 1.46: 2354 1.46 - 1.58: 4366 1.58 - 1.71: 0 1.71 - 1.83: 76 Bond restraints: 9835 Sorted by residual: bond pdb=" CB TRP A 277 " pdb=" CG TRP A 277 " ideal model delta sigma weight residual 1.498 1.432 0.066 3.10e-02 1.04e+03 4.56e+00 bond pdb=" C THR B 243 " pdb=" N GLY B 244 " ideal model delta sigma weight residual 1.330 1.313 0.017 8.50e-03 1.38e+04 4.01e+00 bond pdb=" CA GLY B 244 " pdb=" C GLY B 244 " ideal model delta sigma weight residual 1.520 1.508 0.012 7.30e-03 1.88e+04 2.63e+00 bond pdb=" CB ASP B 76 " pdb=" CG ASP B 76 " ideal model delta sigma weight residual 1.516 1.476 0.040 2.50e-02 1.60e+03 2.62e+00 bond pdb=" CG1 ILE B 273 " pdb=" CD1 ILE B 273 " ideal model delta sigma weight residual 1.513 1.455 0.058 3.90e-02 6.57e+02 2.21e+00 ... (remaining 9830 not shown) Histogram of bond angle deviations from ideal: 95.55 - 103.27: 96 103.27 - 111.00: 3684 111.00 - 118.72: 4154 118.72 - 126.44: 5259 126.44 - 134.17: 179 Bond angle restraints: 13372 Sorted by residual: angle pdb=" C12 HNO R 501 " pdb=" C14 HNO R 501 " pdb=" N15 HNO R 501 " ideal model delta sigma weight residual 101.46 119.34 -17.88 3.00e+00 1.11e-01 3.55e+01 angle pdb=" N15 HNO R 501 " pdb=" C14 HNO R 501 " pdb=" N28 HNO R 501 " ideal model delta sigma weight residual 137.73 122.27 15.46 3.00e+00 1.11e-01 2.66e+01 angle pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " pdb=" CG TYR R 148 " ideal model delta sigma weight residual 113.90 122.27 -8.37 1.80e+00 3.09e-01 2.16e+01 angle pdb=" C GLY R 275 " pdb=" N VAL R 276 " pdb=" CA VAL R 276 " ideal model delta sigma weight residual 120.24 123.02 -2.78 6.30e-01 2.52e+00 1.95e+01 angle pdb=" CB MET B 61 " pdb=" CG MET B 61 " pdb=" SD MET B 61 " ideal model delta sigma weight residual 112.70 102.01 10.69 3.00e+00 1.11e-01 1.27e+01 ... (remaining 13367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.59: 5511 24.59 - 49.18: 200 49.18 - 73.77: 33 73.77 - 98.35: 8 98.35 - 122.94: 1 Dihedral angle restraints: 5753 sinusoidal: 2332 harmonic: 3421 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -24.13 -61.87 1 1.00e+01 1.00e-02 5.07e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -146.08 -33.92 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -144.37 58.37 1 1.00e+01 1.00e-02 4.56e+01 ... (remaining 5750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1309 0.077 - 0.154: 157 0.154 - 0.231: 10 0.231 - 0.308: 8 0.308 - 0.385: 6 Chirality restraints: 1490 Sorted by residual: chirality pdb=" C14 CLR R 506 " pdb=" C13 CLR R 506 " pdb=" C15 CLR R 506 " pdb=" C8 CLR R 506 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" C14 CLR R 508 " pdb=" C13 CLR R 508 " pdb=" C15 CLR R 508 " pdb=" C8 CLR R 508 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" C14 CLR R 505 " pdb=" C13 CLR R 505 " pdb=" C15 CLR R 505 " pdb=" C8 CLR R 505 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 1487 not shown) Planarity restraints: 1658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 357 " 0.023 2.00e-02 2.50e+03 2.77e-02 1.15e+01 pdb=" CG HIS A 357 " -0.058 2.00e-02 2.50e+03 pdb=" ND1 HIS A 357 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 HIS A 357 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS A 357 " -0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS A 357 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 148 " -0.032 2.00e-02 2.50e+03 2.20e-02 9.66e+00 pdb=" CG TYR R 148 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR R 148 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR R 148 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR R 148 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR R 148 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR R 148 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR R 148 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 234 " -0.008 2.00e-02 2.50e+03 1.66e-02 4.83e+00 pdb=" CG PHE B 234 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE B 234 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE B 234 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE B 234 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE B 234 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 234 " -0.003 2.00e-02 2.50e+03 ... (remaining 1655 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 241 2.68 - 3.24: 9542 3.24 - 3.79: 16369 3.79 - 4.35: 22661 4.35 - 4.90: 36150 Nonbonded interactions: 84963 Sorted by model distance: nonbonded pdb=" OE2 GLU P 9 " pdb=" OH TYR R 152 " model vdw 2.126 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.140 2.440 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.157 2.440 nonbonded pdb=" OH TYR A 253 " pdb=" O LYS A 307 " model vdw 2.180 2.440 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.186 2.440 ... (remaining 84958 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: 0.610 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: 3.320 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.960 Find NCS groups from input model: 0.270 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:13.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 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 : 0.006 0.066 9835 Z= 0.413 Angle : 0.849 17.880 13372 Z= 0.449 Chirality : 0.058 0.385 1490 Planarity : 0.005 0.045 1658 Dihedral : 13.345 122.944 3523 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.09 % 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 (0.23), residues: 1154 helix: -0.60 (0.22), residues: 454 sheet: -0.48 (0.29), residues: 265 loop : -0.31 (0.31), residues: 435 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 192 time to evaluate : 1.146 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 193 average time/residue: 1.3721 time to fit residues: 281.8386 Evaluate side-chains 147 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 1.079 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.2632 time to fit residues: 2.1843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 177 ASN R 180 HIS R 221 GLN R 302 ASN R 363 HIS R 407 ASN A 14 ASN A 262 GLN A 278 ASN A 371 ASN A 387 HIS B 155 ASN B 220 GLN N 5 GLN N 82 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9835 Z= 0.221 Angle : 0.556 6.996 13372 Z= 0.293 Chirality : 0.042 0.182 1490 Planarity : 0.004 0.043 1658 Dihedral : 7.091 111.001 1349 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.24), residues: 1154 helix: 0.38 (0.23), residues: 456 sheet: -0.21 (0.30), residues: 261 loop : 0.00 (0.32), residues: 437 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 151 time to evaluate : 1.092 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 9 residues processed: 163 average time/residue: 1.3092 time to fit residues: 227.9522 Evaluate side-chains 142 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 1.131 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.2555 time to fit residues: 2.1247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 263 GLN R 374 HIS A 292 ASN B 91 HIS ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 9835 Z= 0.218 Angle : 0.526 6.917 13372 Z= 0.281 Chirality : 0.041 0.163 1490 Planarity : 0.004 0.041 1658 Dihedral : 6.887 110.576 1349 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.09 % 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: 0.37 (0.25), residues: 1154 helix: 0.78 (0.24), residues: 454 sheet: -0.14 (0.30), residues: 256 loop : 0.15 (0.32), residues: 444 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 1.052 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 153 average time/residue: 1.3358 time to fit residues: 218.5448 Evaluate side-chains 144 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 1.153 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 0.4379 time to fit residues: 4.1535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 11 optimal weight: 0.1980 chunk 49 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 29 optimal weight: 0.3980 chunk 92 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 263 GLN A 59 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9835 Z= 0.180 Angle : 0.499 6.018 13372 Z= 0.265 Chirality : 0.040 0.184 1490 Planarity : 0.004 0.058 1658 Dihedral : 6.669 109.683 1349 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 2.67 % 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: 0.55 (0.25), residues: 1154 helix: 0.97 (0.24), residues: 456 sheet: -0.08 (0.30), residues: 256 loop : 0.20 (0.32), residues: 442 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.057 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 153 average time/residue: 1.3102 time to fit residues: 214.6297 Evaluate side-chains 146 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 4 average time/residue: 0.1451 time to fit residues: 2.4114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 0.3980 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 99 optimal weight: 20.0000 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 263 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.056 9835 Z= 0.370 Angle : 0.601 8.488 13372 Z= 0.315 Chirality : 0.044 0.209 1490 Planarity : 0.005 0.053 1658 Dihedral : 6.944 107.494 1349 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.09 % 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: 0.44 (0.25), residues: 1154 helix: 0.88 (0.24), residues: 454 sheet: -0.19 (0.31), residues: 254 loop : 0.18 (0.32), residues: 446 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 1.159 Fit side-chains outliers start: 29 outliers final: 17 residues processed: 155 average time/residue: 1.2880 time to fit residues: 213.9733 Evaluate side-chains 150 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.4606 time to fit residues: 3.1721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 27 optimal weight: 0.0370 chunk 111 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 263 GLN A 267 GLN B 220 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 9835 Z= 0.326 Angle : 0.579 7.673 13372 Z= 0.305 Chirality : 0.043 0.187 1490 Planarity : 0.005 0.044 1658 Dihedral : 6.963 108.232 1349 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 3.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.09 % 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 (0.25), residues: 1154 helix: 0.91 (0.24), residues: 454 sheet: -0.25 (0.31), residues: 256 loop : 0.12 (0.32), residues: 444 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 1.114 Fit side-chains outliers start: 34 outliers final: 17 residues processed: 157 average time/residue: 1.3548 time to fit residues: 227.8895 Evaluate side-chains 147 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 1.199 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 4 average time/residue: 0.7010 time to fit residues: 4.7332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 68 optimal weight: 0.0770 chunk 44 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 263 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9835 Z= 0.177 Angle : 0.516 8.365 13372 Z= 0.273 Chirality : 0.040 0.175 1490 Planarity : 0.004 0.040 1658 Dihedral : 6.735 109.232 1349 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 2.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.54 (0.25), residues: 1154 helix: 1.11 (0.24), residues: 454 sheet: -0.20 (0.31), residues: 256 loop : 0.11 (0.32), residues: 444 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 138 time to evaluate : 1.084 Fit side-chains outliers start: 27 outliers final: 15 residues processed: 157 average time/residue: 1.2420 time to fit residues: 210.1351 Evaluate side-chains 150 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 1.159 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 4 average time/residue: 0.2016 time to fit residues: 2.7408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 54 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 87 optimal weight: 0.4980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 263 GLN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 9835 Z= 0.168 Angle : 0.522 10.507 13372 Z= 0.271 Chirality : 0.040 0.150 1490 Planarity : 0.004 0.044 1658 Dihedral : 6.592 108.947 1349 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 2.47 % 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: 0.55 (0.25), residues: 1154 helix: 1.07 (0.24), residues: 464 sheet: -0.16 (0.30), residues: 260 loop : 0.13 (0.32), residues: 430 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 1.040 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 158 average time/residue: 1.2211 time to fit residues: 207.4879 Evaluate side-chains 151 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.1412 time to fit residues: 1.9209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 0.4980 chunk 67 optimal weight: 0.2980 chunk 109 optimal weight: 0.0670 overall best weight: 0.5320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 9835 Z= 0.162 Angle : 0.514 10.539 13372 Z= 0.267 Chirality : 0.040 0.193 1490 Planarity : 0.004 0.040 1658 Dihedral : 6.484 108.822 1349 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 2.27 % 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: 0.65 (0.25), residues: 1154 helix: 1.20 (0.24), residues: 459 sheet: -0.11 (0.30), residues: 260 loop : 0.12 (0.32), residues: 435 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 1.167 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 17 residues processed: 157 average time/residue: 1.1912 time to fit residues: 201.3151 Evaluate side-chains 149 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 1.156 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 4 average time/residue: 0.1591 time to fit residues: 2.5173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 9835 Z= 0.202 Angle : 0.539 10.411 13372 Z= 0.278 Chirality : 0.041 0.243 1490 Planarity : 0.004 0.039 1658 Dihedral : 6.521 108.736 1349 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1154 helix: 1.24 (0.24), residues: 458 sheet: -0.14 (0.30), residues: 260 loop : 0.18 (0.32), residues: 436 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 1.148 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 15 residues processed: 146 average time/residue: 1.2121 time to fit residues: 190.1212 Evaluate side-chains 146 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.016 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.1398 time to fit residues: 1.8224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 0.2980 chunk 5 optimal weight: 0.0030 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.198645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.142682 restraints weight = 9980.258| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.24 r_work: 0.3600 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 9835 Z= 0.155 Angle : 0.513 10.287 13372 Z= 0.265 Chirality : 0.040 0.231 1490 Planarity : 0.004 0.039 1658 Dihedral : 6.397 108.713 1349 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.25), residues: 1154 helix: 1.32 (0.24), residues: 459 sheet: -0.07 (0.31), residues: 251 loop : 0.23 (0.32), residues: 444 =============================================================================== Job complete usr+sys time: 4309.36 seconds wall clock time: 77 minutes 5.95 seconds (4625.95 seconds total)