Starting phenix.real_space_refine on Thu Mar 14 14:43:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jim_36318/03_2024/8jim_36318_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jim_36318/03_2024/8jim_36318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jim_36318/03_2024/8jim_36318.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jim_36318/03_2024/8jim_36318.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jim_36318/03_2024/8jim_36318_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jim_36318/03_2024/8jim_36318_neut_updated.pdb" } resolution = 2.98 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= 0.019 sd= 0.095 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 5779 2.51 5 N 1538 2.21 5 O 1665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "D GLU 14": "OE1" <-> "OE2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D ARG 205": "NH1" <-> "NH2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "D GLU 297": "OE1" <-> "OE2" Residue "S TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 160": "NH1" <-> "NH2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 218": "NH1" <-> "NH2" Residue "S GLU 220": "OE1" <-> "OE2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E ARG 111": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 142": "NH1" <-> "NH2" Residue "E GLU 190": "OE1" <-> "OE2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "E ARG 218": "NH1" <-> "NH2" Residue "E ARG 222": "NH1" <-> "NH2" Residue "E ARG 228": "NH1" <-> "NH2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 251": "NH1" <-> "NH2" Residue "E ARG 253": "NH1" <-> "NH2" Residue "E ARG 270": "NH1" <-> "NH2" 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: 9051 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1813 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "E" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2370 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'AW9': 1, 'CLR': 1} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 2} Time building chain proxies: 5.06, per 1000 atoms: 0.56 Number of scatterers: 9051 At special positions: 0 Unit cell: (93.5, 122.4, 137.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 1665 8.00 N 1538 7.00 C 5779 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS E 18 " - pdb=" SG CYS E 183 " distance=2.04 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 266 " distance=2.03 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS E 177 " 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=0, symmetry=0 Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 1.8 seconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 12 sheets defined 28.3% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'B' and resid 2 through 23 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 8 through 22 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'D' and resid 12 through 26 Processing helix chain 'D' and resid 46 through 53 Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 242 through 254 Processing helix chain 'D' and resid 271 through 277 removed outlier: 3.778A pdb=" N GLU D 275 " --> pdb=" O LYS D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 285 No H-bonds generated for 'chain 'D' and resid 283 through 285' Processing helix chain 'D' and resid 296 through 310 removed outlier: 4.033A pdb=" N LEU D 310 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 350 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'E' and resid 26 through 53 Proline residue: E 31 - end of helix removed outlier: 4.309A pdb=" N LEU E 43 " --> pdb=" O ILE E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 88 removed outlier: 3.741A pdb=" N LEU E 69 " --> pdb=" O PHE E 65 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE E 78 " --> pdb=" O PHE E 74 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N CYS E 79 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU E 80 " --> pdb=" O LEU E 76 " (cutoff:3.500A) Proline residue: E 81 - end of helix Processing helix chain 'E' and resid 96 through 100 removed outlier: 3.834A pdb=" N CYS E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 96 through 100' Processing helix chain 'E' and resid 107 through 110 No H-bonds generated for 'chain 'E' and resid 107 through 110' Processing helix chain 'E' and resid 112 through 119 removed outlier: 4.133A pdb=" N PHE E 117 " --> pdb=" O GLY E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 129 removed outlier: 4.672A pdb=" N TYR E 126 " --> pdb=" O ALA E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 138 No H-bonds generated for 'chain 'E' and resid 136 through 138' Processing helix chain 'E' and resid 141 through 158 removed outlier: 4.001A pdb=" N LEU E 158 " --> pdb=" O ILE E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 188 through 192 Processing helix chain 'E' and resid 198 through 215 removed outlier: 4.131A pdb=" N ILE E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 243 removed outlier: 3.925A pdb=" N ALA E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE E 230 " --> pdb=" O ILE E 226 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR E 231 " --> pdb=" O LYS E 227 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE E 240 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL E 241 " --> pdb=" O ALA E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 260 removed outlier: 3.590A pdb=" N VAL E 250 " --> pdb=" O PRO E 246 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 270 removed outlier: 3.614A pdb=" N ARG E 270 " --> pdb=" O GLU E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 279 removed outlier: 3.866A pdb=" N ILE E 278 " --> pdb=" O LEU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 288 Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.950A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.039A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.885A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 220 through 223 removed outlier: 4.473A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.961A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 276 through 278 Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.851A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 319 through 323 removed outlier: 6.742A pdb=" N ILE D 264 " --> pdb=" O TYR D 320 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N HIS D 322 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU D 266 " --> pdb=" O HIS D 322 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA D 220 " --> pdb=" O LYS D 35 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 115 through 117 removed outlier: 5.714A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 146 through 148 removed outlier: 7.378A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR S 243 " --> pdb=" O TYR S 227 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 155 through 160 323 hydrogen bonds defined for protein. 906 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: 2.53 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1462 1.31 - 1.44: 2571 1.44 - 1.57: 5114 1.57 - 1.70: 0 1.70 - 1.83: 100 Bond restraints: 9247 Sorted by residual: bond pdb=" CA SER S 193 " pdb=" CB SER S 193 " ideal model delta sigma weight residual 1.533 1.460 0.073 1.60e-02 3.91e+03 2.07e+01 bond pdb=" C ILE E 230 " pdb=" O ILE E 230 " ideal model delta sigma weight residual 1.237 1.285 -0.048 1.17e-02 7.31e+03 1.68e+01 bond pdb=" CA ALA E 229 " pdb=" CB ALA E 229 " ideal model delta sigma weight residual 1.528 1.465 0.064 1.66e-02 3.63e+03 1.47e+01 bond pdb=" C ARG E 228 " pdb=" O ARG E 228 " ideal model delta sigma weight residual 1.237 1.281 -0.044 1.19e-02 7.06e+03 1.40e+01 bond pdb=" C ALA E 229 " pdb=" O ALA E 229 " ideal model delta sigma weight residual 1.236 1.282 -0.046 1.26e-02 6.30e+03 1.33e+01 ... (remaining 9242 not shown) Histogram of bond angle deviations from ideal: 98.66 - 105.74: 141 105.74 - 112.81: 4853 112.81 - 119.89: 3171 119.89 - 126.97: 4239 126.97 - 134.04: 109 Bond angle restraints: 12513 Sorted by residual: angle pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta sigma weight residual 122.60 109.58 13.02 1.88e+00 2.83e-01 4.80e+01 angle pdb=" N ARG S 191 " pdb=" CA ARG S 191 " pdb=" C ARG S 191 " ideal model delta sigma weight residual 108.00 99.52 8.48 1.48e+00 4.57e-01 3.28e+01 angle pdb=" N SER S 193 " pdb=" CA SER S 193 " pdb=" CB SER S 193 " ideal model delta sigma weight residual 110.61 102.05 8.56 1.51e+00 4.39e-01 3.21e+01 angle pdb=" C ASN S 194 " pdb=" CA ASN S 194 " pdb=" CB ASN S 194 " ideal model delta sigma weight residual 109.89 117.74 -7.85 1.60e+00 3.91e-01 2.41e+01 angle pdb=" N ALA E 229 " pdb=" CA ALA E 229 " pdb=" C ALA E 229 " ideal model delta sigma weight residual 111.82 106.75 5.07 1.16e+00 7.43e-01 1.91e+01 ... (remaining 12508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 4864 15.46 - 30.91: 514 30.91 - 46.37: 124 46.37 - 61.82: 21 61.82 - 77.28: 7 Dihedral angle restraints: 5530 sinusoidal: 2218 harmonic: 3312 Sorted by residual: dihedral pdb=" CB CYS E 18 " pdb=" SG CYS E 18 " pdb=" SG CYS E 183 " pdb=" CB CYS E 183 " ideal model delta sinusoidal sigma weight residual 93.00 49.73 43.27 1 1.00e+01 1.00e-02 2.61e+01 dihedral pdb=" CA ASP B 290 " pdb=" C ASP B 290 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " ideal model delta harmonic sigma weight residual 180.00 156.89 23.11 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA PHE E 52 " pdb=" C PHE E 52 " pdb=" N CYS E 53 " pdb=" CA CYS E 53 " ideal model delta harmonic sigma weight residual -180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 5527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 830 0.041 - 0.082: 432 0.082 - 0.123: 110 0.123 - 0.164: 29 0.164 - 0.205: 6 Chirality restraints: 1407 Sorted by residual: chirality pdb=" CA ILE E 233 " pdb=" N ILE E 233 " pdb=" C ILE E 233 " pdb=" CB ILE E 233 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA VAL E 235 " pdb=" N VAL E 235 " pdb=" C VAL E 235 " pdb=" CB VAL E 235 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" CB VAL S 64 " pdb=" CA VAL S 64 " pdb=" CG1 VAL S 64 " pdb=" CG2 VAL S 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.97e-01 ... (remaining 1404 not shown) Planarity restraints: 1578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 227 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.46e+00 pdb=" C LYS E 227 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS E 227 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG E 228 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.025 2.00e-02 2.50e+03 1.98e-02 7.85e+00 pdb=" CG TYR B 105 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET S 192 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.80e+00 pdb=" C MET S 192 " -0.045 2.00e-02 2.50e+03 pdb=" O MET S 192 " 0.017 2.00e-02 2.50e+03 pdb=" N SER S 193 " 0.016 2.00e-02 2.50e+03 ... (remaining 1575 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1643 2.77 - 3.30: 8281 3.30 - 3.83: 13663 3.83 - 4.37: 16409 4.37 - 4.90: 29646 Nonbonded interactions: 69642 Sorted by model distance: nonbonded pdb=" O LEU S 174 " pdb=" O ARG S 191 " model vdw 2.232 3.040 nonbonded pdb=" O ILE S 100 " pdb=" OG SER S 105 " model vdw 2.234 2.440 nonbonded pdb=" O SER E 214 " pdb=" OG SER E 214 " model vdw 2.257 2.440 nonbonded pdb=" OG SER S 161 " pdb=" OG1 THR S 210 " model vdw 2.261 2.440 nonbonded pdb=" NZ LYS B 89 " pdb=" OD1 ASP D 20 " model vdw 2.287 2.520 ... (remaining 69637 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: 0.750 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: 3.990 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 27.110 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:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 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 : 0.007 0.073 9247 Z= 0.444 Angle : 0.905 13.021 12513 Z= 0.533 Chirality : 0.052 0.205 1407 Planarity : 0.004 0.050 1578 Dihedral : 13.511 77.278 3378 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.75 % Favored : 94.16 % Rotamer: Outliers : 0.41 % Allowed : 1.01 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.23), residues: 1130 helix: -0.53 (0.28), residues: 329 sheet: -0.41 (0.31), residues: 271 loop : -2.23 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP S 47 HIS 0.009 0.002 HIS S 35 PHE 0.025 0.002 PHE E 52 TYR 0.049 0.003 TYR B 105 ARG 0.007 0.001 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 162 time to evaluate : 1.000 Fit side-chains REVERT: B 217 MET cc_start: 0.7942 (ptt) cc_final: 0.7734 (ptt) REVERT: C 48 ASP cc_start: 0.6571 (p0) cc_final: 0.6366 (p0) REVERT: D 24 ARG cc_start: 0.7980 (ttp-110) cc_final: 0.7729 (ttp80) REVERT: D 270 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7866 (mtmp) REVERT: S 46 GLU cc_start: 0.7826 (pm20) cc_final: 0.7585 (pm20) REVERT: E 269 TYR cc_start: 0.7639 (m-80) cc_final: 0.7306 (m-80) REVERT: E 274 LEU cc_start: 0.7943 (tp) cc_final: 0.7734 (tm) REVERT: E 282 PHE cc_start: 0.7587 (m-80) cc_final: 0.7049 (m-10) outliers start: 4 outliers final: 2 residues processed: 166 average time/residue: 1.2054 time to fit residues: 213.5774 Evaluate side-chains 135 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain E residue 231 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 0.0980 chunk 47 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 268 ASN B 340 ASN S 82 GLN S 194 ASN E 161 HIS E 189 HIS E 223 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9247 Z= 0.171 Angle : 0.594 7.638 12513 Z= 0.312 Chirality : 0.042 0.143 1407 Planarity : 0.004 0.038 1578 Dihedral : 6.211 89.890 1307 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.43 % Allowed : 9.84 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.24), residues: 1130 helix: 0.20 (0.29), residues: 338 sheet: -0.22 (0.31), residues: 277 loop : -1.94 (0.24), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.010 0.001 HIS E 161 PHE 0.032 0.001 PHE E 255 TYR 0.013 0.001 TYR B 105 ARG 0.003 0.000 ARG E 101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 130 time to evaluate : 1.029 Fit side-chains REVERT: C 48 ASP cc_start: 0.6922 (p0) cc_final: 0.6699 (p0) REVERT: D 24 ARG cc_start: 0.7961 (ttp-110) cc_final: 0.7710 (ttm170) REVERT: D 195 HIS cc_start: 0.7650 (OUTLIER) cc_final: 0.7439 (t70) REVERT: S 67 ARG cc_start: 0.7753 (mtm180) cc_final: 0.7470 (mtm180) REVERT: E 282 PHE cc_start: 0.7490 (m-80) cc_final: 0.7146 (m-10) outliers start: 24 outliers final: 9 residues processed: 141 average time/residue: 1.2342 time to fit residues: 185.1644 Evaluate side-chains 129 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 119 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 281 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 340 ASN S 113 GLN E 161 HIS E 223 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9247 Z= 0.239 Angle : 0.607 7.442 12513 Z= 0.317 Chirality : 0.044 0.148 1407 Planarity : 0.004 0.036 1578 Dihedral : 5.824 87.679 1304 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.64 % Allowed : 12.47 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.24), residues: 1130 helix: 0.36 (0.29), residues: 343 sheet: -0.11 (0.31), residues: 279 loop : -1.79 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.011 0.001 HIS E 161 PHE 0.034 0.002 PHE E 255 TYR 0.021 0.002 TYR B 105 ARG 0.006 0.000 ARG E 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 0.815 Fit side-chains REVERT: B 258 ASP cc_start: 0.7694 (p0) cc_final: 0.7481 (p0) REVERT: D 24 ARG cc_start: 0.7953 (ttp-110) cc_final: 0.7682 (ttm170) REVERT: S 60 TYR cc_start: 0.7878 (m-80) cc_final: 0.7675 (m-80) REVERT: S 67 ARG cc_start: 0.7670 (mtm180) cc_final: 0.7351 (mtm180) REVERT: E 269 TYR cc_start: 0.7743 (m-80) cc_final: 0.7532 (m-80) outliers start: 26 outliers final: 16 residues processed: 138 average time/residue: 1.2533 time to fit residues: 184.1662 Evaluate side-chains 136 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 251 ARG Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 281 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 102 optimal weight: 0.0980 chunk 108 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 96 optimal weight: 0.0670 chunk 29 optimal weight: 0.0060 chunk 90 optimal weight: 3.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN B 340 ASN E 161 HIS E 223 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9247 Z= 0.141 Angle : 0.528 6.833 12513 Z= 0.276 Chirality : 0.041 0.139 1407 Planarity : 0.003 0.039 1578 Dihedral : 5.386 82.125 1304 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.84 % Allowed : 14.30 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.74 (0.25), residues: 1130 helix: 0.74 (0.30), residues: 334 sheet: -0.03 (0.31), residues: 278 loop : -1.60 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.010 0.001 HIS E 161 PHE 0.033 0.001 PHE E 38 TYR 0.008 0.001 TYR S 190 ARG 0.004 0.000 ARG E 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 119 time to evaluate : 1.130 Fit side-chains REVERT: B 258 ASP cc_start: 0.7560 (p0) cc_final: 0.7274 (p0) REVERT: D 24 ARG cc_start: 0.7924 (ttp-110) cc_final: 0.7698 (ttp-110) REVERT: D 195 HIS cc_start: 0.7762 (t70) cc_final: 0.7522 (t70) REVERT: D 248 LYS cc_start: 0.8040 (tppt) cc_final: 0.7292 (mtpm) REVERT: D 270 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8180 (mtmp) REVERT: S 46 GLU cc_start: 0.8011 (pm20) cc_final: 0.7506 (pm20) REVERT: S 67 ARG cc_start: 0.7699 (mtm180) cc_final: 0.7432 (mtm180) REVERT: E 269 TYR cc_start: 0.7596 (m-80) cc_final: 0.7369 (m-80) outliers start: 28 outliers final: 10 residues processed: 133 average time/residue: 1.2287 time to fit residues: 174.2811 Evaluate side-chains 126 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 251 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 9247 Z= 0.544 Angle : 0.750 8.954 12513 Z= 0.389 Chirality : 0.050 0.176 1407 Planarity : 0.005 0.037 1578 Dihedral : 6.103 75.311 1304 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.06 % Allowed : 16.53 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.24), residues: 1130 helix: 0.26 (0.30), residues: 338 sheet: -0.15 (0.31), residues: 283 loop : -1.81 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP S 47 HIS 0.012 0.002 HIS E 161 PHE 0.039 0.003 PHE E 255 TYR 0.048 0.003 TYR B 105 ARG 0.006 0.001 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 125 time to evaluate : 1.025 Fit side-chains REVERT: B 258 ASP cc_start: 0.7643 (p0) cc_final: 0.7338 (p0) REVERT: D 248 LYS cc_start: 0.8057 (tppt) cc_final: 0.7330 (mtpm) REVERT: D 270 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8351 (mtmp) REVERT: S 191 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.3937 (mpp-170) outliers start: 40 outliers final: 23 residues processed: 149 average time/residue: 1.2069 time to fit residues: 192.2436 Evaluate side-chains 148 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 191 ARG Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 292 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN E 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9247 Z= 0.161 Angle : 0.557 7.533 12513 Z= 0.290 Chirality : 0.042 0.142 1407 Planarity : 0.003 0.039 1578 Dihedral : 5.455 71.569 1304 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.25 % Allowed : 19.17 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1130 helix: 0.67 (0.30), residues: 338 sheet: -0.03 (0.31), residues: 280 loop : -1.61 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP S 47 HIS 0.011 0.001 HIS E 161 PHE 0.034 0.001 PHE E 38 TYR 0.016 0.001 TYR S 95 ARG 0.003 0.000 ARG D 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 122 time to evaluate : 0.911 Fit side-chains REVERT: B 258 ASP cc_start: 0.7524 (p0) cc_final: 0.7177 (p0) REVERT: D 248 LYS cc_start: 0.7896 (tppt) cc_final: 0.7221 (mtpm) REVERT: D 270 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8308 (mtmp) REVERT: S 67 ARG cc_start: 0.7666 (mtm180) cc_final: 0.7400 (mtm180) outliers start: 32 outliers final: 15 residues processed: 142 average time/residue: 1.2215 time to fit residues: 184.8027 Evaluate side-chains 134 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 292 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 91 optimal weight: 0.0980 chunk 60 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9247 Z= 0.160 Angle : 0.546 8.435 12513 Z= 0.282 Chirality : 0.042 0.144 1407 Planarity : 0.003 0.039 1578 Dihedral : 5.223 68.292 1304 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.25 % Allowed : 19.88 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1130 helix: 0.82 (0.31), residues: 333 sheet: 0.06 (0.31), residues: 280 loop : -1.51 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.011 0.001 HIS E 161 PHE 0.034 0.001 PHE E 38 TYR 0.012 0.001 TYR B 105 ARG 0.004 0.000 ARG D 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 117 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: B 258 ASP cc_start: 0.7483 (p0) cc_final: 0.7194 (p0) REVERT: D 248 LYS cc_start: 0.7808 (tppt) cc_final: 0.7219 (mtpm) REVERT: D 270 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8378 (mtmp) outliers start: 32 outliers final: 16 residues processed: 140 average time/residue: 1.1580 time to fit residues: 173.4401 Evaluate side-chains 131 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 292 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 0.3980 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 84 optimal weight: 0.0000 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN E 45 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9247 Z= 0.137 Angle : 0.529 8.671 12513 Z= 0.273 Chirality : 0.041 0.145 1407 Planarity : 0.003 0.040 1578 Dihedral : 5.042 65.688 1304 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.33 % Allowed : 20.89 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.44 (0.25), residues: 1130 helix: 1.02 (0.31), residues: 328 sheet: 0.14 (0.31), residues: 282 loop : -1.40 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.011 0.001 HIS E 161 PHE 0.034 0.001 PHE E 38 TYR 0.009 0.001 TYR S 190 ARG 0.004 0.000 ARG E 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: B 258 ASP cc_start: 0.7490 (p0) cc_final: 0.7158 (p0) REVERT: D 248 LYS cc_start: 0.7786 (tppt) cc_final: 0.7267 (mtpm) REVERT: D 263 SER cc_start: 0.8005 (m) cc_final: 0.7713 (t) REVERT: D 270 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8368 (mtmp) outliers start: 23 outliers final: 14 residues processed: 129 average time/residue: 1.2195 time to fit residues: 167.9465 Evaluate side-chains 126 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 292 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9247 Z= 0.168 Angle : 0.549 8.875 12513 Z= 0.282 Chirality : 0.042 0.140 1407 Planarity : 0.003 0.040 1578 Dihedral : 5.017 61.502 1304 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.13 % Allowed : 21.20 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.39 (0.25), residues: 1130 helix: 1.01 (0.31), residues: 333 sheet: 0.14 (0.31), residues: 283 loop : -1.34 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 47 HIS 0.012 0.001 HIS E 161 PHE 0.033 0.001 PHE E 38 TYR 0.014 0.001 TYR B 105 ARG 0.006 0.000 ARG E 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: B 258 ASP cc_start: 0.7467 (p0) cc_final: 0.7121 (p0) REVERT: D 270 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8415 (mtpt) REVERT: E 53 CYS cc_start: 0.5797 (p) cc_final: 0.5310 (m) outliers start: 21 outliers final: 17 residues processed: 132 average time/residue: 1.1904 time to fit residues: 167.9920 Evaluate side-chains 131 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 0.1980 chunk 70 optimal weight: 3.9990 chunk 94 optimal weight: 0.0970 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 161 HIS E 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9247 Z= 0.301 Angle : 0.632 9.455 12513 Z= 0.327 Chirality : 0.045 0.153 1407 Planarity : 0.004 0.045 1578 Dihedral : 5.329 59.524 1304 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.13 % Allowed : 21.81 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.49 (0.25), residues: 1130 helix: 0.86 (0.31), residues: 337 sheet: 0.08 (0.31), residues: 282 loop : -1.36 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP S 36 HIS 0.012 0.002 HIS E 161 PHE 0.034 0.002 PHE E 255 TYR 0.026 0.002 TYR B 105 ARG 0.005 0.000 ARG E 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6939 (ptm-80) REVERT: B 258 ASP cc_start: 0.7536 (p0) cc_final: 0.7192 (p0) REVERT: D 248 LYS cc_start: 0.8023 (tppt) cc_final: 0.7256 (mtpm) REVERT: D 270 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8379 (mtmp) REVERT: S 191 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.3829 (mpp-170) outliers start: 21 outliers final: 16 residues processed: 142 average time/residue: 1.2466 time to fit residues: 188.8571 Evaluate side-chains 145 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 191 ARG Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 0.0050 chunk 5 optimal weight: 1.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.144743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.108192 restraints weight = 13967.830| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.47 r_work: 0.3328 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9247 Z= 0.147 Angle : 0.553 9.188 12513 Z= 0.286 Chirality : 0.041 0.149 1407 Planarity : 0.003 0.042 1578 Dihedral : 4.975 54.856 1304 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.93 % Allowed : 22.62 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.25), residues: 1130 helix: 1.06 (0.31), residues: 333 sheet: 0.21 (0.31), residues: 280 loop : -1.36 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.011 0.001 HIS E 161 PHE 0.033 0.001 PHE E 38 TYR 0.009 0.001 TYR B 105 ARG 0.007 0.000 ARG E 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3611.46 seconds wall clock time: 64 minutes 17.04 seconds (3857.04 seconds total)