Starting phenix.real_space_refine on Thu Jul 2 11:45:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7trs_26102/07_2026/7trs_26102.cif Found real_map, /net/cci-nas-00/data/ceres_data/7trs_26102/07_2026/7trs_26102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7trs_26102/07_2026/7trs_26102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7trs_26102/07_2026/7trs_26102.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7trs_26102/07_2026/7trs_26102.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7trs_26102/07_2026/7trs_26102.cif" model { file = "/net/cci-nas-00/data/ceres_data/7trs_26102/07_2026/7trs_26102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7trs_26102/07_2026/7trs_26102.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.002 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 62 5.16 5 C 5471 2.51 5 N 1443 2.21 5 O 1595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8571 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2549 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "G" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 391 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "H" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1768 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1748 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "R" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2105 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'ACH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.36, per 1000 atoms: 0.16 Number of scatterers: 8571 At special positions: 0 Unit cell: (90.47, 119.52, 121.18, 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 62 16.00 O 1595 8.00 N 1443 7.00 C 5471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 426 " - pdb=" SG CYS R 429 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.47 Conformation dependent library (CDL) restraints added in 319.2 milliseconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 38.3% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.685A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.513A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.507A pdb=" N SER H 31 " --> pdb=" O ALA H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 56 removed outlier: 4.000A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.577A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.888A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.677A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.053A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.942A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'R' and resid 33 through 60 Processing helix chain 'R' and resid 61 through 64 Processing helix chain 'R' and resid 65 through 84 removed outlier: 4.123A pdb=" N PHE R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU R 71 " --> pdb=" O ASN R 67 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA R 77 " --> pdb=" O SER R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 96 Processing helix chain 'R' and resid 101 through 136 Processing helix chain 'R' and resid 139 through 144 Processing helix chain 'R' and resid 145 through 176 Proline residue: R 166 - end of helix removed outlier: 5.249A pdb=" N GLN R 172 " --> pdb=" O ILE R 168 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N PHE R 173 " --> pdb=" O LEU R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 191 removed outlier: 3.890A pdb=" N LEU R 190 " --> pdb=" O ILE R 187 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER R 191 " --> pdb=" O GLN R 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 187 through 191' Processing helix chain 'R' and resid 192 through 204 removed outlier: 3.582A pdb=" N THR R 196 " --> pdb=" O ASN R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 221 Processing helix chain 'R' and resid 393 through 424 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 426 through 430 removed outlier: 3.514A pdb=" N CYS R 429 " --> pdb=" O CYS R 426 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE R 430 " --> pdb=" O GLN R 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 426 through 430' Processing helix chain 'R' and resid 431 through 448 removed outlier: 3.974A pdb=" N CYS R 442 " --> pdb=" O GLY R 438 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR R 443 " --> pdb=" O TYR R 439 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL R 444 " --> pdb=" O TRP R 440 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN R 445 " --> pdb=" O LEU R 441 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER R 446 " --> pdb=" O CYS R 442 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR R 447 " --> pdb=" O TYR R 443 " (cutoff:3.500A) Processing helix chain 'R' and resid 448 through 454 Processing helix chain 'R' and resid 457 through 466 removed outlier: 3.571A pdb=" N LYS R 461 " --> pdb=" O ASN R 457 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 52 Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.662A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.914A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.509A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.480A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.521A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.294A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB1, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.590A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.590A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.604A pdb=" N ILE H 189 " --> pdb=" O TRP H 176 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 155 through 160 Processing sheet with id=AB5, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.153A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1266 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: 0.91 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2677 1.34 - 1.46: 1799 1.46 - 1.58: 4188 1.58 - 1.69: 0 1.69 - 1.81: 89 Bond restraints: 8753 Sorted by residual: bond pdb=" C5 ACH R 501 " pdb=" O4 ACH R 501 " ideal model delta sigma weight residual 1.335 1.455 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" C THR R 414 " pdb=" N PRO R 415 " ideal model delta sigma weight residual 1.335 1.374 -0.039 1.38e-02 5.25e+03 8.16e+00 bond pdb=" CA THR R 414 " pdb=" C THR R 414 " ideal model delta sigma weight residual 1.522 1.544 -0.022 1.26e-02 6.30e+03 3.03e+00 bond pdb=" CB PRO R 415 " pdb=" CG PRO R 415 " ideal model delta sigma weight residual 1.492 1.408 0.084 5.00e-02 4.00e+02 2.82e+00 bond pdb=" C2 ACH R 501 " pdb=" N1 ACH R 501 " ideal model delta sigma weight residual 1.506 1.473 0.033 2.00e-02 2.50e+03 2.74e+00 ... (remaining 8748 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 11460 1.79 - 3.58: 364 3.58 - 5.37: 59 5.37 - 7.15: 13 7.15 - 8.94: 5 Bond angle restraints: 11901 Sorted by residual: angle pdb=" CA PRO R 415 " pdb=" N PRO R 415 " pdb=" CD PRO R 415 " ideal model delta sigma weight residual 112.00 107.57 4.43 1.40e+00 5.10e-01 1.00e+01 angle pdb=" CA ARG B 150 " pdb=" CB ARG B 150 " pdb=" CG ARG B 150 " ideal model delta sigma weight residual 114.10 120.36 -6.26 2.00e+00 2.50e-01 9.80e+00 angle pdb=" CA THR R 414 " pdb=" CB THR R 414 " pdb=" CG2 THR R 414 " ideal model delta sigma weight residual 110.50 115.78 -5.28 1.70e+00 3.46e-01 9.64e+00 angle pdb=" C ARG B 19 " pdb=" N ASP B 20 " pdb=" CA ASP B 20 " ideal model delta sigma weight residual 122.06 116.30 5.76 1.86e+00 2.89e-01 9.58e+00 angle pdb=" C PHE A 307 " pdb=" N GLU A 308 " pdb=" CA GLU A 308 " ideal model delta sigma weight residual 121.58 115.58 6.00 1.95e+00 2.63e-01 9.46e+00 ... (remaining 11896 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 4765 17.18 - 34.35: 311 34.35 - 51.53: 57 51.53 - 68.71: 6 68.71 - 85.88: 8 Dihedral angle restraints: 5147 sinusoidal: 1890 harmonic: 3257 Sorted by residual: dihedral pdb=" CB CYS H 159 " pdb=" SG CYS H 159 " pdb=" SG CYS H 229 " pdb=" CB CYS H 229 " ideal model delta sinusoidal sigma weight residual 93.00 51.52 41.48 1 1.00e+01 1.00e-02 2.41e+01 dihedral pdb=" CA TYR H 101 " pdb=" C TYR H 101 " pdb=" N TYR H 102 " pdb=" CA TYR H 102 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 162.47 17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 5144 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1068 0.060 - 0.121: 264 0.121 - 0.181: 44 0.181 - 0.241: 4 0.241 - 0.302: 1 Chirality restraints: 1381 Sorted by residual: chirality pdb=" CA THR R 414 " pdb=" N THR R 414 " pdb=" C THR R 414 " pdb=" CB THR R 414 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CB VAL R 33 " pdb=" CA VAL R 33 " pdb=" CG1 VAL R 33 " pdb=" CG2 VAL R 33 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB ILE H 70 " pdb=" CA ILE H 70 " pdb=" CG1 ILE H 70 " pdb=" CG2 ILE H 70 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.14e-01 ... (remaining 1378 not shown) Planarity restraints: 1496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H 199 " 0.047 5.00e-02 4.00e+02 7.22e-02 8.34e+00 pdb=" N PRO H 200 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO H 200 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO H 200 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO B 236 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 40 " 0.039 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO H 41 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " 0.033 5.00e-02 4.00e+02 ... (remaining 1493 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1753 2.77 - 3.31: 7679 3.31 - 3.84: 14695 3.84 - 4.37: 17115 4.37 - 4.90: 30166 Nonbonded interactions: 71408 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.243 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.273 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.289 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.304 3.040 nonbonded pdb=" OE2 GLU A 308 " pdb=" OG1 THR A 321 " model vdw 2.321 3.040 ... (remaining 71403 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.990 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.490 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:5.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 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 0.120 8757 Z= 0.260 Angle : 0.777 8.943 11909 Z= 0.425 Chirality : 0.054 0.302 1381 Planarity : 0.006 0.072 1496 Dihedral : 12.244 85.881 3033 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.23), residues: 1105 helix: -1.01 (0.22), residues: 388 sheet: -0.23 (0.29), residues: 302 loop : -0.54 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 178 TYR 0.016 0.002 TYR A 302 PHE 0.023 0.002 PHE R 204 TRP 0.026 0.002 TRP R 164 HIS 0.008 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.26 ( 8753) covalent geometry : angle 0.77546 / 0.42 (11901) SS BOND : bond 0.00254 / 0.12 ( 4) SS BOND : angle 1.75817 / 0.79 ( 8) hydrogen bonds : bond 0.21787 / 14.77 ( 432) hydrogen bonds : angle 7.94157 / 5.66 ( 1266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 ASN cc_start: 0.8948 (m-40) cc_final: 0.8741 (m-40) REVERT: B 23 LYS cc_start: 0.9285 (tptp) cc_final: 0.9084 (tptp) REVERT: H 46 GLU cc_start: 0.7958 (tt0) cc_final: 0.7727 (tt0) REVERT: A 208 ARG cc_start: 0.8403 (ttm-80) cc_final: 0.8135 (ttt90) REVERT: A 306 GLN cc_start: 0.8949 (mm110) cc_final: 0.8479 (mp10) REVERT: A 345 LYS cc_start: 0.8628 (ttmt) cc_final: 0.8316 (ttmt) REVERT: R 106 ASP cc_start: 0.7081 (m-30) cc_final: 0.6767 (t0) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.5770 time to fit residues: 114.0182 Evaluate side-chains 131 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN G 18 GLN H 3 GLN H 186 GLN H 231 GLN A 331 ASN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.090117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.063110 restraints weight = 20095.594| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.04 r_work: 0.2925 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8757 Z= 0.234 Angle : 0.661 10.370 11909 Z= 0.346 Chirality : 0.044 0.178 1381 Planarity : 0.005 0.055 1496 Dihedral : 4.560 20.455 1206 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.75 % Allowed : 12.22 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.24), residues: 1105 helix: 0.96 (0.26), residues: 381 sheet: -0.02 (0.30), residues: 283 loop : -0.41 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 160 TYR 0.013 0.002 TYR H 190 PHE 0.015 0.002 PHE B 253 TRP 0.018 0.002 TRP B 211 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.23 ( 8753) covalent geometry : angle 0.66077 / 0.35 (11901) SS BOND : bond 0.00288 / 0.14 ( 4) SS BOND : angle 1.01447 / 0.49 ( 8) hydrogen bonds : bond 0.04989 / 3.43 ( 432) hydrogen bonds : angle 5.01444 / 3.67 ( 1266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9387 (tptp) cc_final: 0.9126 (tptp) REVERT: B 32 GLN cc_start: 0.8741 (mt0) cc_final: 0.8486 (mt0) REVERT: B 130 GLU cc_start: 0.8756 (mp0) cc_final: 0.8491 (mp0) REVERT: H 13 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8388 (mm-40) REVERT: H 180 ARG cc_start: 0.9245 (mtt-85) cc_final: 0.8985 (mtt-85) REVERT: A 205 ARG cc_start: 0.8583 (mmp80) cc_final: 0.8382 (mmp80) REVERT: A 208 ARG cc_start: 0.8461 (ttm-80) cc_final: 0.8125 (ttt90) REVERT: A 306 GLN cc_start: 0.9120 (mm110) cc_final: 0.8668 (mp10) REVERT: A 345 LYS cc_start: 0.8665 (ttmt) cc_final: 0.8414 (ttmt) REVERT: R 98 TRP cc_start: 0.7721 (t-100) cc_final: 0.7519 (t-100) REVERT: R 143 ARG cc_start: 0.6671 (mmm-85) cc_final: 0.6418 (tmt90) REVERT: R 152 MET cc_start: 0.7500 (mmp) cc_final: 0.7190 (mmt) REVERT: R 223 ARG cc_start: 0.8363 (ptp-170) cc_final: 0.8097 (ptp-170) REVERT: R 396 ARG cc_start: 0.7454 (tpt170) cc_final: 0.7204 (mtt180) REVERT: R 448 ILE cc_start: 0.7450 (pt) cc_final: 0.7202 (pp) outliers start: 25 outliers final: 9 residues processed: 149 average time/residue: 0.5926 time to fit residues: 92.8016 Evaluate side-chains 128 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 212 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN H 231 GLN R 188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.090626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.063693 restraints weight = 19718.687| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.99 r_work: 0.2939 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8757 Z= 0.174 Angle : 0.599 9.095 11909 Z= 0.310 Chirality : 0.042 0.163 1381 Planarity : 0.004 0.051 1496 Dihedral : 4.303 18.127 1206 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.75 % Allowed : 15.86 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.25), residues: 1105 helix: 1.71 (0.26), residues: 382 sheet: -0.06 (0.29), residues: 286 loop : -0.36 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 160 TYR 0.016 0.001 TYR H 190 PHE 0.016 0.001 PHE R 84 TRP 0.016 0.001 TRP B 211 HIS 0.007 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 8753) covalent geometry : angle 0.59892 / 0.31 (11901) SS BOND : bond 0.00237 / 0.12 ( 4) SS BOND : angle 0.72378 / 0.32 ( 8) hydrogen bonds : bond 0.04189 / 2.89 ( 432) hydrogen bonds : angle 4.61492 / 3.40 ( 1266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9325 (tptp) cc_final: 0.9099 (tptp) REVERT: B 130 GLU cc_start: 0.8801 (mp0) cc_final: 0.8547 (mp0) REVERT: G 19 LEU cc_start: 0.9722 (mm) cc_final: 0.9479 (mm) REVERT: H 13 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8407 (mm-40) REVERT: H 180 ARG cc_start: 0.9292 (mtt-85) cc_final: 0.8986 (mtt-85) REVERT: A 306 GLN cc_start: 0.9094 (mm110) cc_final: 0.8689 (mp10) REVERT: A 345 LYS cc_start: 0.8696 (ttmt) cc_final: 0.8438 (ttmt) REVERT: A 349 LYS cc_start: 0.8449 (mtmm) cc_final: 0.8234 (tptp) REVERT: R 121 MET cc_start: 0.8654 (mmm) cc_final: 0.8371 (mmp) REVERT: R 143 ARG cc_start: 0.6839 (mmm-85) cc_final: 0.6622 (mtm180) REVERT: R 152 MET cc_start: 0.7539 (mmp) cc_final: 0.7185 (mmt) REVERT: R 177 LYS cc_start: 0.7560 (pptt) cc_final: 0.7326 (pptt) REVERT: R 223 ARG cc_start: 0.8378 (ptp-170) cc_final: 0.8156 (ptp-170) REVERT: R 396 ARG cc_start: 0.7480 (tpt170) cc_final: 0.7206 (mtt180) outliers start: 25 outliers final: 8 residues processed: 138 average time/residue: 0.5885 time to fit residues: 85.5285 Evaluate side-chains 121 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 188 GLN Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 441 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 61 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 68 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN H 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.091037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.064085 restraints weight = 19959.782| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.01 r_work: 0.2949 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8757 Z= 0.151 Angle : 0.579 8.116 11909 Z= 0.301 Chirality : 0.042 0.157 1381 Planarity : 0.004 0.048 1496 Dihedral : 4.187 17.605 1206 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.87 % Allowed : 17.84 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.25), residues: 1105 helix: 1.99 (0.27), residues: 380 sheet: -0.13 (0.29), residues: 286 loop : -0.34 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 160 TYR 0.015 0.001 TYR H 190 PHE 0.012 0.001 PHE R 84 TRP 0.024 0.002 TRP R 98 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 8753) covalent geometry : angle 0.57930 / 0.30 (11901) SS BOND : bond 0.00264 / 0.13 ( 4) SS BOND : angle 0.65106 / 0.30 ( 8) hydrogen bonds : bond 0.03775 / 2.60 ( 432) hydrogen bonds : angle 4.42040 / 3.27 ( 1266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9275 (tptp) cc_final: 0.9040 (tptp) REVERT: B 130 GLU cc_start: 0.8799 (mp0) cc_final: 0.8534 (mp0) REVERT: H 180 ARG cc_start: 0.9306 (mtt-85) cc_final: 0.8999 (mtt-85) REVERT: H 244 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8873 (ttpp) REVERT: A 306 GLN cc_start: 0.9086 (mm110) cc_final: 0.8646 (mp10) REVERT: A 345 LYS cc_start: 0.8676 (ttmt) cc_final: 0.8416 (ttmt) REVERT: A 349 LYS cc_start: 0.8522 (mtmm) cc_final: 0.8289 (tptp) REVERT: R 86 MET cc_start: 0.7434 (mmt) cc_final: 0.7208 (mmt) REVERT: R 98 TRP cc_start: 0.7181 (t-100) cc_final: 0.6801 (t-100) REVERT: R 143 ARG cc_start: 0.6916 (mmm-85) cc_final: 0.6603 (tmt90) REVERT: R 152 MET cc_start: 0.7669 (mmp) cc_final: 0.7356 (mmt) REVERT: R 396 ARG cc_start: 0.7455 (tpt170) cc_final: 0.7181 (mtt180) REVERT: R 452 CYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7662 (p) outliers start: 17 outliers final: 6 residues processed: 130 average time/residue: 0.6388 time to fit residues: 87.1901 Evaluate side-chains 120 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 452 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 70 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN H 231 GLN R 188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.090048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.063101 restraints weight = 19870.275| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.97 r_work: 0.2922 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8757 Z= 0.191 Angle : 0.596 8.604 11909 Z= 0.310 Chirality : 0.042 0.153 1381 Planarity : 0.004 0.048 1496 Dihedral : 4.209 17.413 1206 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.41 % Allowed : 18.28 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.25), residues: 1105 helix: 2.01 (0.27), residues: 380 sheet: -0.14 (0.29), residues: 293 loop : -0.29 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 160 TYR 0.013 0.001 TYR H 190 PHE 0.012 0.001 PHE B 253 TRP 0.023 0.002 TRP R 440 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 ( 8753) covalent geometry : angle 0.59631 / 0.31 (11901) SS BOND : bond 0.00194 / 0.10 ( 4) SS BOND : angle 0.69419 / 0.30 ( 8) hydrogen bonds : bond 0.03874 / 2.67 ( 432) hydrogen bonds : angle 4.39735 / 3.25 ( 1266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9294 (tptp) cc_final: 0.9065 (tptp) REVERT: B 130 GLU cc_start: 0.8807 (mp0) cc_final: 0.8537 (mp0) REVERT: G 19 LEU cc_start: 0.9718 (mm) cc_final: 0.9465 (mm) REVERT: H 76 LYS cc_start: 0.9091 (mtmm) cc_final: 0.8789 (mtmm) REVERT: H 180 ARG cc_start: 0.9347 (mtt-85) cc_final: 0.9021 (mtt-85) REVERT: H 244 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8909 (ttpp) REVERT: A 306 GLN cc_start: 0.9077 (mm110) cc_final: 0.8697 (mp10) REVERT: A 345 LYS cc_start: 0.8669 (ttmt) cc_final: 0.8407 (ttmt) REVERT: A 349 LYS cc_start: 0.8597 (mtmm) cc_final: 0.8322 (tptp) REVERT: R 136 LYS cc_start: 0.7494 (mmmm) cc_final: 0.7218 (mmtp) REVERT: R 143 ARG cc_start: 0.6874 (mmm-85) cc_final: 0.6541 (tmt90) REVERT: R 152 MET cc_start: 0.7667 (mmp) cc_final: 0.7375 (mmt) REVERT: R 396 ARG cc_start: 0.7496 (tpt170) cc_final: 0.7234 (mtt180) REVERT: R 440 TRP cc_start: 0.8251 (t-100) cc_final: 0.7932 (t-100) outliers start: 31 outliers final: 9 residues processed: 143 average time/residue: 0.5684 time to fit residues: 85.4013 Evaluate side-chains 124 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 452 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 82 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN H 231 GLN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.091461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.064698 restraints weight = 19720.330| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.96 r_work: 0.2963 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8757 Z= 0.130 Angle : 0.584 9.099 11909 Z= 0.300 Chirality : 0.041 0.153 1381 Planarity : 0.004 0.048 1496 Dihedral : 4.044 17.074 1206 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.98 % Allowed : 19.93 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.25), residues: 1105 helix: 2.05 (0.27), residues: 381 sheet: -0.06 (0.29), residues: 291 loop : -0.24 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 160 TYR 0.016 0.001 TYR H 190 PHE 0.011 0.001 PHE B 199 TRP 0.022 0.002 TRP R 98 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 8753) covalent geometry : angle 0.58416 / 0.30 (11901) SS BOND : bond 0.00212 / 0.11 ( 4) SS BOND : angle 0.54048 / 0.24 ( 8) hydrogen bonds : bond 0.03467 / 2.39 ( 432) hydrogen bonds : angle 4.29246 / 3.18 ( 1266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9274 (tptp) cc_final: 0.9038 (tptp) REVERT: H 76 LYS cc_start: 0.9029 (mtmm) cc_final: 0.8752 (mtmm) REVERT: H 180 ARG cc_start: 0.9401 (mtt-85) cc_final: 0.9063 (mtt-85) REVERT: H 244 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8878 (ttpp) REVERT: A 306 GLN cc_start: 0.9054 (mm110) cc_final: 0.8664 (mp10) REVERT: A 345 LYS cc_start: 0.8659 (ttmt) cc_final: 0.8393 (ttmt) REVERT: A 349 LYS cc_start: 0.8598 (mtmm) cc_final: 0.8329 (tptp) REVERT: R 136 LYS cc_start: 0.7496 (mmmm) cc_final: 0.7225 (mmtp) REVERT: R 143 ARG cc_start: 0.6969 (mmm-85) cc_final: 0.6638 (tmt90) REVERT: R 152 MET cc_start: 0.7673 (mmp) cc_final: 0.7401 (mmt) REVERT: R 396 ARG cc_start: 0.7497 (tpt170) cc_final: 0.7263 (mtt180) outliers start: 18 outliers final: 6 residues processed: 129 average time/residue: 0.6530 time to fit residues: 88.5606 Evaluate side-chains 120 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 452 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN H 231 GLN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.090974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.064245 restraints weight = 19944.260| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.97 r_work: 0.2951 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8757 Z= 0.152 Angle : 0.603 10.986 11909 Z= 0.310 Chirality : 0.041 0.154 1381 Planarity : 0.004 0.050 1496 Dihedral : 4.051 16.779 1206 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.76 % Allowed : 21.26 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.25), residues: 1105 helix: 1.97 (0.27), residues: 381 sheet: -0.07 (0.29), residues: 293 loop : -0.14 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 160 TYR 0.015 0.001 TYR H 190 PHE 0.011 0.001 PHE B 199 TRP 0.026 0.002 TRP R 440 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 8753) covalent geometry : angle 0.60288 / 0.31 (11901) SS BOND : bond 0.00192 / 0.10 ( 4) SS BOND : angle 0.58795 / 0.26 ( 8) hydrogen bonds : bond 0.03556 / 2.45 ( 432) hydrogen bonds : angle 4.25583 / 3.13 ( 1266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9280 (tptp) cc_final: 0.9046 (tptp) REVERT: H 76 LYS cc_start: 0.9035 (mtmm) cc_final: 0.8763 (mtmm) REVERT: H 180 ARG cc_start: 0.9406 (mtt-85) cc_final: 0.9094 (mtt-85) REVERT: H 244 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8937 (ttpp) REVERT: A 306 GLN cc_start: 0.9066 (mm110) cc_final: 0.8693 (mp10) REVERT: A 345 LYS cc_start: 0.8669 (ttmt) cc_final: 0.8397 (ttmt) REVERT: A 349 LYS cc_start: 0.8621 (mtmm) cc_final: 0.8329 (tptp) REVERT: R 86 MET cc_start: 0.7205 (mmt) cc_final: 0.6677 (mmt) REVERT: R 136 LYS cc_start: 0.7457 (mmmm) cc_final: 0.7201 (mmtm) REVERT: R 143 ARG cc_start: 0.6990 (mmm-85) cc_final: 0.6629 (tmt90) REVERT: R 152 MET cc_start: 0.7724 (mmp) cc_final: 0.7475 (mmt) REVERT: R 396 ARG cc_start: 0.7531 (tpt170) cc_final: 0.7305 (mtt180) outliers start: 16 outliers final: 8 residues processed: 128 average time/residue: 0.7528 time to fit residues: 101.3289 Evaluate side-chains 123 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain R residue 107 LEU Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 452 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN H 231 GLN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.089762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.062813 restraints weight = 19964.881| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.97 r_work: 0.2912 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8757 Z= 0.223 Angle : 0.658 11.991 11909 Z= 0.340 Chirality : 0.043 0.154 1381 Planarity : 0.005 0.062 1496 Dihedral : 4.282 18.767 1206 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.20 % Allowed : 21.59 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.25), residues: 1105 helix: 1.86 (0.27), residues: 382 sheet: -0.06 (0.29), residues: 291 loop : -0.16 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 223 TYR 0.013 0.002 TYR H 190 PHE 0.012 0.001 PHE B 253 TRP 0.026 0.002 TRP R 108 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 ( 8753) covalent geometry : angle 0.65747 / 0.34 (11901) SS BOND : bond 0.00191 / 0.10 ( 4) SS BOND : angle 0.80272 / 0.36 ( 8) hydrogen bonds : bond 0.03934 / 2.71 ( 432) hydrogen bonds : angle 4.39688 / 3.23 ( 1266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9305 (tptp) cc_final: 0.9062 (tptp) REVERT: B 130 GLU cc_start: 0.8807 (mp0) cc_final: 0.8590 (mp0) REVERT: H 76 LYS cc_start: 0.9084 (mtmm) cc_final: 0.8813 (mtmm) REVERT: H 180 ARG cc_start: 0.9430 (mtt-85) cc_final: 0.9120 (mtt-85) REVERT: H 244 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.8910 (ttpp) REVERT: A 306 GLN cc_start: 0.9104 (mm110) cc_final: 0.8709 (mp10) REVERT: A 345 LYS cc_start: 0.8683 (ttmt) cc_final: 0.8407 (ttmt) REVERT: A 349 LYS cc_start: 0.8690 (mtmm) cc_final: 0.8349 (tptp) REVERT: R 86 MET cc_start: 0.7199 (mmt) cc_final: 0.6616 (mmt) REVERT: R 143 ARG cc_start: 0.6956 (mmm-85) cc_final: 0.6574 (tmt90) REVERT: R 152 MET cc_start: 0.7655 (mmp) cc_final: 0.7356 (mmt) REVERT: R 223 ARG cc_start: 0.8305 (ptp-110) cc_final: 0.7709 (ptp-170) REVERT: R 396 ARG cc_start: 0.7566 (tpt170) cc_final: 0.7293 (mtt180) outliers start: 20 outliers final: 13 residues processed: 128 average time/residue: 0.7413 time to fit residues: 99.8205 Evaluate side-chains 126 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 107 LEU Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 413 TRP Chi-restraints excluded: chain R residue 452 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 3 optimal weight: 0.4980 chunk 31 optimal weight: 4.9990 chunk 70 optimal weight: 0.0050 chunk 85 optimal weight: 7.9990 chunk 8 optimal weight: 0.4980 chunk 83 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.091541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.064762 restraints weight = 19854.647| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.98 r_work: 0.2956 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8757 Z= 0.143 Angle : 0.637 12.861 11909 Z= 0.326 Chirality : 0.042 0.154 1381 Planarity : 0.004 0.053 1496 Dihedral : 4.100 18.563 1206 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.76 % Allowed : 22.25 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.26), residues: 1105 helix: 2.01 (0.27), residues: 376 sheet: -0.00 (0.30), residues: 289 loop : -0.17 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 223 TYR 0.015 0.001 TYR H 190 PHE 0.011 0.001 PHE B 199 TRP 0.027 0.002 TRP R 108 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 8753) covalent geometry : angle 0.63714 / 0.33 (11901) SS BOND : bond 0.00214 / 0.11 ( 4) SS BOND : angle 0.57553 / 0.26 ( 8) hydrogen bonds : bond 0.03492 / 2.40 ( 432) hydrogen bonds : angle 4.26120 / 3.13 ( 1266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9298 (tptp) cc_final: 0.9057 (tptp) REVERT: B 130 GLU cc_start: 0.8800 (mp0) cc_final: 0.8581 (mp0) REVERT: H 76 LYS cc_start: 0.9031 (mtmm) cc_final: 0.8769 (mtmm) REVERT: H 180 ARG cc_start: 0.9405 (mtt-85) cc_final: 0.9127 (mtt-85) REVERT: A 25 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7728 (tm-30) REVERT: A 306 GLN cc_start: 0.9097 (mm110) cc_final: 0.8715 (mp10) REVERT: A 345 LYS cc_start: 0.8666 (ttmt) cc_final: 0.8359 (ttmt) REVERT: A 349 LYS cc_start: 0.8688 (mtmm) cc_final: 0.8374 (tptp) REVERT: R 86 MET cc_start: 0.7126 (mmt) cc_final: 0.6607 (mmt) REVERT: R 143 ARG cc_start: 0.6958 (mmm-85) cc_final: 0.6567 (tmt90) REVERT: R 152 MET cc_start: 0.7716 (mmp) cc_final: 0.7432 (mmt) REVERT: R 396 ARG cc_start: 0.7571 (tpt170) cc_final: 0.7335 (mtt180) outliers start: 16 outliers final: 12 residues processed: 134 average time/residue: 0.7393 time to fit residues: 104.1266 Evaluate side-chains 128 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain R residue 107 LEU Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 444 VAL Chi-restraints excluded: chain R residue 452 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 39 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 46 optimal weight: 0.0570 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.091021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.064203 restraints weight = 20015.685| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.99 r_work: 0.2945 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8757 Z= 0.161 Angle : 0.665 13.327 11909 Z= 0.338 Chirality : 0.042 0.177 1381 Planarity : 0.004 0.052 1496 Dihedral : 4.114 19.099 1206 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.76 % Allowed : 22.58 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.26), residues: 1105 helix: 1.97 (0.27), residues: 376 sheet: 0.04 (0.30), residues: 301 loop : -0.13 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 38 TYR 0.025 0.001 TYR A 296 PHE 0.011 0.001 PHE B 199 TRP 0.027 0.002 TRP R 108 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 8753) covalent geometry : angle 0.66486 / 0.34 (11901) SS BOND : bond 0.00191 / 0.10 ( 4) SS BOND : angle 0.63944 / 0.28 ( 8) hydrogen bonds : bond 0.03589 / 2.47 ( 432) hydrogen bonds : angle 4.25461 / 3.12 ( 1266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9276 (tptp) cc_final: 0.9031 (tptp) REVERT: B 61 MET cc_start: 0.9046 (ppp) cc_final: 0.8836 (pp-130) REVERT: H 76 LYS cc_start: 0.9040 (mtmm) cc_final: 0.8785 (mtmm) REVERT: H 180 ARG cc_start: 0.9423 (mtt-85) cc_final: 0.9143 (mtt-85) REVERT: A 25 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7758 (tm-30) REVERT: A 205 ARG cc_start: 0.8896 (mmm160) cc_final: 0.8625 (mmp80) REVERT: A 306 GLN cc_start: 0.9097 (mm110) cc_final: 0.8720 (mp10) REVERT: A 345 LYS cc_start: 0.8673 (ttmt) cc_final: 0.8363 (ttmt) REVERT: A 349 LYS cc_start: 0.8707 (mtmm) cc_final: 0.8367 (tptp) REVERT: R 86 MET cc_start: 0.7083 (mmt) cc_final: 0.6488 (mmt) REVERT: R 143 ARG cc_start: 0.6933 (mmm-85) cc_final: 0.6565 (tmt90) REVERT: R 152 MET cc_start: 0.7727 (mmp) cc_final: 0.7429 (mmt) REVERT: R 223 ARG cc_start: 0.8243 (ptp90) cc_final: 0.7618 (ptp-170) REVERT: R 396 ARG cc_start: 0.7572 (tpt170) cc_final: 0.7333 (mtt180) outliers start: 16 outliers final: 11 residues processed: 128 average time/residue: 0.7499 time to fit residues: 100.9640 Evaluate side-chains 126 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain R residue 107 LEU Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 452 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 21 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 3 optimal weight: 0.0980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.092752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.066207 restraints weight = 19904.815| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.96 r_work: 0.2997 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8757 Z= 0.124 Angle : 0.656 13.919 11909 Z= 0.330 Chirality : 0.041 0.153 1381 Planarity : 0.004 0.054 1496 Dihedral : 3.968 19.160 1206 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.54 % Allowed : 23.02 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.26), residues: 1105 helix: 2.04 (0.28), residues: 376 sheet: 0.14 (0.30), residues: 299 loop : -0.13 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 38 TYR 0.016 0.001 TYR H 190 PHE 0.008 0.001 PHE B 199 TRP 0.028 0.002 TRP R 108 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 8753) covalent geometry : angle 0.65626 / 0.33 (11901) SS BOND : bond 0.00229 / 0.12 ( 4) SS BOND : angle 0.56525 / 0.25 ( 8) hydrogen bonds : bond 0.03247 / 2.23 ( 432) hydrogen bonds : angle 4.16500 / 3.07 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3414.76 seconds wall clock time: 59 minutes 3.53 seconds (3543.53 seconds total)