Starting phenix.real_space_refine on Thu Mar 14 19:55:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duq_30866/03_2024/7duq_30866_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duq_30866/03_2024/7duq_30866.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duq_30866/03_2024/7duq_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_30866/03_2024/7duq_30866_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duq_30866/03_2024/7duq_30866_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duq_30866/03_2024/7duq_30866.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duq_30866/03_2024/7duq_30866.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duq_30866/03_2024/7duq_30866_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duq_30866/03_2024/7duq_30866_trim_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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-dev-5265/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: 5.70, per 1000 atoms: 0.59 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: 4.05 Conformation dependent library (CDL) restraints added in 1.6 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: 1.78 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: 2.92 Time building geometry restraints manager: 4.42 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: 5871 24.59 - 49.18: 227 49.18 - 73.77: 36 73.77 - 98.35: 8 98.35 - 122.94: 3 Dihedral angle restraints: 6145 sinusoidal: 2724 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 6142 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: 0.530 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: 3.010 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 29.870 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.810 ------------------------------------------------------------------------------- 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 : 13.617 122.944 3915 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 % Allowed : 2.67 % Favored : 97.04 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.032 0.003 HIS A 357 PHE 0.034 0.003 PHE B 234 TYR 0.052 0.002 TYR R 148 ARG 0.006 0.001 ARG B 22 *********************** 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 : 1.122 Fit side-chains revert: symmetry clash REVERT: R 265 ILE cc_start: 0.7346 (tp) cc_final: 0.7087 (tp) REVERT: R 293 ASP cc_start: 0.6091 (p0) cc_final: 0.5821 (p0) REVERT: A 299 GLU cc_start: 0.5918 (mt-10) cc_final: 0.5600 (tp30) REVERT: B 176 GLN cc_start: 0.8410 (tt0) cc_final: 0.8119 (tt0) REVERT: B 188 MET cc_start: 0.8517 (mmm) cc_final: 0.8235 (mmm) REVERT: B 220 GLN cc_start: 0.7838 (mt0) cc_final: 0.7214 (mt0) REVERT: B 273 ILE cc_start: 0.8114 (mt) cc_final: 0.7902 (mp) REVERT: G 21 MET cc_start: 0.4481 (ptp) cc_final: 0.3995 (pmm) outliers start: 3 outliers final: 3 residues processed: 193 average time/residue: 1.3451 time to fit residues: 276.1128 Evaluate side-chains 150 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 147 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 59 TYR 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: 1.9990 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 90 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 176 GLN N 5 GLN N 82 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9835 Z= 0.212 Angle : 0.557 6.982 13372 Z= 0.291 Chirality : 0.042 0.178 1490 Planarity : 0.004 0.043 1658 Dihedral : 7.790 59.908 1747 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.07 % Allowed : 10.37 % Favored : 87.56 % 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: -0.03 (0.24), residues: 1154 helix: 0.34 (0.23), residues: 456 sheet: -0.24 (0.30), residues: 256 loop : -0.03 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.007 0.001 HIS R 180 PHE 0.017 0.002 PHE A 273 TYR 0.034 0.002 TYR R 148 ARG 0.010 0.001 ARG R 40 *********************** 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: 21 poor density : 153 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: P 9 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6936 (mt-10) REVERT: R 265 ILE cc_start: 0.7373 (tp) cc_final: 0.7135 (tp) REVERT: G 21 MET cc_start: 0.4165 (ptp) cc_final: 0.3708 (pmm) REVERT: N 103 PHE cc_start: 0.8206 (m-80) cc_final: 0.7948 (m-80) outliers start: 21 outliers final: 7 residues processed: 164 average time/residue: 1.2840 time to fit residues: 224.6300 Evaluate side-chains 143 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 GLU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain N residue 63 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 20.0000 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 374 HIS A 292 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9835 Z= 0.287 Angle : 0.558 7.770 13372 Z= 0.297 Chirality : 0.043 0.207 1490 Planarity : 0.005 0.041 1658 Dihedral : 7.445 59.474 1743 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.37 % Allowed : 13.23 % Favored : 84.40 % 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: 0.24 (0.25), residues: 1154 helix: 0.68 (0.24), residues: 453 sheet: -0.28 (0.30), residues: 255 loop : 0.11 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 243 HIS 0.007 0.001 HIS A 357 PHE 0.019 0.002 PHE R 230 TYR 0.033 0.002 TYR R 148 ARG 0.008 0.001 ARG R 40 *********************** 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: 24 poor density : 139 time to evaluate : 1.194 Fit side-chains revert: symmetry clash REVERT: P 9 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6879 (mt-10) REVERT: R 211 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7391 (tp-100) REVERT: R 414 ARG cc_start: 0.7357 (ttm110) cc_final: 0.7076 (ttm110) REVERT: A 20 ARG cc_start: 0.7151 (mtp85) cc_final: 0.6840 (mtm-85) REVERT: A 309 GLU cc_start: 0.5640 (pm20) cc_final: 0.5410 (pm20) REVERT: G 21 MET cc_start: 0.4102 (ptp) cc_final: 0.3718 (pmm) outliers start: 24 outliers final: 13 residues processed: 154 average time/residue: 1.2222 time to fit residues: 201.6390 Evaluate side-chains 145 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 GLU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 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 263 GLN B 91 HIS ** B 156 GLN ** 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: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9835 Z= 0.208 Angle : 0.507 6.685 13372 Z= 0.269 Chirality : 0.041 0.177 1490 Planarity : 0.004 0.041 1658 Dihedral : 7.027 55.912 1743 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.17 % Allowed : 14.81 % Favored : 83.02 % 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: 0.48 (0.25), residues: 1154 helix: 0.94 (0.24), residues: 453 sheet: -0.14 (0.30), residues: 256 loop : 0.17 (0.32), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.016 0.001 PHE R 230 TYR 0.028 0.002 TYR R 148 ARG 0.008 0.000 ARG R 40 *********************** 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 163 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 9 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6904 (mt-10) REVERT: R 41 GLU cc_start: 0.7031 (tp30) cc_final: 0.6791 (tp30) REVERT: R 211 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7366 (tp-100) REVERT: R 414 ARG cc_start: 0.7314 (ttm110) cc_final: 0.7041 (ttm110) REVERT: A 20 ARG cc_start: 0.7059 (mtp85) cc_final: 0.6756 (mtm-85) REVERT: B 220 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7339 (mt0) REVERT: N 103 PHE cc_start: 0.8285 (m-80) cc_final: 0.8073 (m-80) outliers start: 22 outliers final: 11 residues processed: 152 average time/residue: 1.2559 time to fit residues: 203.9904 Evaluate side-chains 141 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 GLU Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain N residue 63 SER 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: 2.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 180 HIS R 263 GLN A 267 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2051 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= 0.312 Angle : 0.559 7.720 13372 Z= 0.295 Chirality : 0.043 0.222 1490 Planarity : 0.005 0.045 1658 Dihedral : 7.043 57.108 1743 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.06 % Allowed : 15.70 % Favored : 81.24 % 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: 0.48 (0.25), residues: 1154 helix: 0.96 (0.24), residues: 451 sheet: -0.23 (0.31), residues: 254 loop : 0.21 (0.32), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 243 HIS 0.008 0.001 HIS A 357 PHE 0.020 0.002 PHE R 230 TYR 0.031 0.002 TYR R 148 ARG 0.008 0.000 ARG R 40 *********************** 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: 31 poor density : 134 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: P 9 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6940 (mt-10) REVERT: R 211 GLN cc_start: 0.7655 (mm-40) cc_final: 0.7360 (tp-100) REVERT: R 414 ARG cc_start: 0.7303 (ttm110) cc_final: 0.7010 (ttm110) REVERT: A 20 ARG cc_start: 0.7085 (mtp85) cc_final: 0.6776 (mtm-85) REVERT: B 220 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7295 (mt0) outliers start: 31 outliers final: 14 residues processed: 150 average time/residue: 1.2107 time to fit residues: 194.6687 Evaluate side-chains 142 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 GLU Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 0.0870 chunk 111 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9835 Z= 0.221 Angle : 0.512 6.755 13372 Z= 0.272 Chirality : 0.041 0.174 1490 Planarity : 0.004 0.040 1658 Dihedral : 6.894 57.260 1743 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.75 % Allowed : 15.60 % Favored : 80.65 % 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: 0.50 (0.25), residues: 1154 helix: 1.05 (0.24), residues: 454 sheet: -0.20 (0.31), residues: 256 loop : 0.10 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.001 PHE R 230 TYR 0.028 0.002 TYR R 148 ARG 0.008 0.000 ARG R 40 *********************** 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 169 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 131 time to evaluate : 1.037 Fit side-chains REVERT: R 211 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7363 (tp-100) REVERT: R 345 ILE cc_start: 0.6607 (OUTLIER) cc_final: 0.6402 (mm) REVERT: R 414 ARG cc_start: 0.7285 (ttm110) cc_final: 0.7040 (ttm-80) REVERT: A 20 ARG cc_start: 0.7061 (mtp85) cc_final: 0.6753 (mtm-85) REVERT: A 265 ARG cc_start: 0.7398 (mmm-85) cc_final: 0.7119 (mtp180) REVERT: B 76 ASP cc_start: 0.6624 (OUTLIER) cc_final: 0.6352 (m-30) REVERT: B 220 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.7264 (mt0) REVERT: G 21 MET cc_start: 0.4302 (ptp) cc_final: 0.3741 (pmm) outliers start: 38 outliers final: 20 residues processed: 155 average time/residue: 1.2098 time to fit residues: 201.4943 Evaluate side-chains 151 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 63 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 68 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2324 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= 0.214 Angle : 0.511 6.855 13372 Z= 0.269 Chirality : 0.041 0.169 1490 Planarity : 0.004 0.040 1658 Dihedral : 6.850 57.292 1743 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.16 % Allowed : 16.29 % Favored : 80.55 % 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: 0.54 (0.25), residues: 1154 helix: 1.12 (0.24), residues: 454 sheet: -0.21 (0.31), residues: 256 loop : 0.12 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.001 PHE R 230 TYR 0.028 0.002 TYR R 148 ARG 0.009 0.000 ARG R 40 *********************** 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 166 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 134 time to evaluate : 0.870 Fit side-chains REVERT: R 414 ARG cc_start: 0.7242 (ttm110) cc_final: 0.7002 (ttm-80) REVERT: A 20 ARG cc_start: 0.7097 (mtp85) cc_final: 0.6857 (mtm-85) REVERT: A 265 ARG cc_start: 0.7406 (mmm-85) cc_final: 0.7042 (mtp180) REVERT: B 76 ASP cc_start: 0.6472 (OUTLIER) cc_final: 0.6210 (m-30) REVERT: G 21 MET cc_start: 0.4290 (ptp) cc_final: 0.3791 (pmm) outliers start: 32 outliers final: 19 residues processed: 156 average time/residue: 1.1711 time to fit residues: 196.6444 Evaluate side-chains 150 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 63 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 54 optimal weight: 0.0770 chunk 10 optimal weight: 20.0000 chunk 87 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9835 Z= 0.181 Angle : 0.505 10.236 13372 Z= 0.263 Chirality : 0.041 0.159 1490 Planarity : 0.004 0.040 1658 Dihedral : 6.742 58.985 1743 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.27 % Allowed : 17.87 % Favored : 79.86 % 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: 0.61 (0.25), residues: 1154 helix: 1.18 (0.24), residues: 454 sheet: -0.14 (0.31), residues: 247 loop : 0.10 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 264 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.001 PHE R 230 TYR 0.026 0.002 TYR R 148 ARG 0.008 0.000 ARG R 40 *********************** 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 155 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 1.015 Fit side-chains REVERT: R 414 ARG cc_start: 0.7235 (ttm110) cc_final: 0.6999 (ttm110) REVERT: A 20 ARG cc_start: 0.6991 (mtp85) cc_final: 0.6747 (mtm-85) REVERT: A 265 ARG cc_start: 0.7404 (mmm-85) cc_final: 0.7090 (mtp180) REVERT: B 76 ASP cc_start: 0.6401 (OUTLIER) cc_final: 0.6169 (m-30) REVERT: G 21 MET cc_start: 0.4144 (ptp) cc_final: 0.3593 (pmm) outliers start: 23 outliers final: 18 residues processed: 147 average time/residue: 1.2109 time to fit residues: 190.8997 Evaluate side-chains 149 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 0.4980 chunk 67 optimal weight: 0.0060 chunk 109 optimal weight: 0.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9835 Z= 0.174 Angle : 0.507 10.528 13372 Z= 0.262 Chirality : 0.041 0.213 1490 Planarity : 0.004 0.040 1658 Dihedral : 6.674 59.098 1743 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.17 % Allowed : 18.46 % Favored : 79.37 % 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: 0.63 (0.25), residues: 1154 helix: 1.16 (0.24), residues: 463 sheet: -0.13 (0.31), residues: 252 loop : 0.14 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 264 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.001 PHE R 230 TYR 0.026 0.002 TYR R 148 ARG 0.008 0.000 ARG B 96 *********************** 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 156 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 1.045 Fit side-chains REVERT: R 414 ARG cc_start: 0.7250 (ttm110) cc_final: 0.7031 (ttm110) REVERT: A 20 ARG cc_start: 0.6979 (mtp85) cc_final: 0.6746 (mtm-85) REVERT: A 265 ARG cc_start: 0.7344 (mmm-85) cc_final: 0.7046 (mtp180) REVERT: B 76 ASP cc_start: 0.6412 (OUTLIER) cc_final: 0.6200 (m-30) REVERT: G 21 MET cc_start: 0.4110 (ptp) cc_final: 0.3667 (pmm) outliers start: 22 outliers final: 17 residues processed: 149 average time/residue: 1.1865 time to fit residues: 189.9233 Evaluate side-chains 149 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2579 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= 0.227 Angle : 0.532 10.326 13372 Z= 0.275 Chirality : 0.042 0.253 1490 Planarity : 0.004 0.039 1658 Dihedral : 6.780 56.974 1743 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.37 % Allowed : 18.36 % Favored : 79.27 % 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: 0.67 (0.25), residues: 1154 helix: 1.27 (0.24), residues: 455 sheet: -0.21 (0.30), residues: 261 loop : 0.17 (0.33), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 264 HIS 0.006 0.001 HIS A 357 PHE 0.017 0.001 PHE R 230 TYR 0.027 0.002 TYR R 148 ARG 0.008 0.000 ARG B 96 ********************** 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 153 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.052 Fit side-chains REVERT: R 40 ARG cc_start: 0.7861 (ttm-80) cc_final: 0.7512 (mtp180) REVERT: R 414 ARG cc_start: 0.7262 (ttm110) cc_final: 0.7042 (ttm-80) REVERT: A 20 ARG cc_start: 0.6992 (mtp85) cc_final: 0.6702 (mtm-85) REVERT: A 265 ARG cc_start: 0.7369 (mmm-85) cc_final: 0.7047 (mtp180) REVERT: B 76 ASP cc_start: 0.6496 (OUTLIER) cc_final: 0.6249 (m-30) REVERT: G 21 MET cc_start: 0.4114 (ptp) cc_final: 0.3664 (pmm) outliers start: 24 outliers final: 16 residues processed: 145 average time/residue: 1.1924 time to fit residues: 185.5847 Evaluate side-chains 143 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 91 optimal weight: 0.0370 chunk 38 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.197370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.140560 restraints weight = 9959.776| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.23 r_work: 0.3575 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2701 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= 0.165 Angle : 0.500 10.244 13372 Z= 0.259 Chirality : 0.041 0.229 1490 Planarity : 0.004 0.039 1658 Dihedral : 6.650 59.045 1743 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.88 % Allowed : 18.85 % Favored : 79.27 % 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: 0.78 (0.25), residues: 1154 helix: 1.33 (0.24), residues: 458 sheet: -0.07 (0.31), residues: 250 loop : 0.19 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 264 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE R 230 TYR 0.025 0.001 TYR R 148 ARG 0.007 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4267.60 seconds wall clock time: 75 minutes 56.45 seconds (4556.45 seconds total)