Starting phenix.real_space_refine on Tue Mar 3 20:29:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7trs_26102/03_2026/7trs_26102.cif Found real_map, /net/cci-nas-00/data/ceres_data/7trs_26102/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7trs_26102/03_2026/7trs_26102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7trs_26102/03_2026/7trs_26102.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7trs_26102/03_2026/7trs_26102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7trs_26102/03_2026/7trs_26102.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 1.97, per 1000 atoms: 0.23 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: 0.66 Conformation dependent library (CDL) restraints added in 334.9 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: 0.28 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: 1.38 Time building geometry restraints manager: 0.89 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: 312 34.35 - 51.53: 57 51.53 - 68.71: 6 68.71 - 85.88: 8 Dihedral angle restraints: 5148 sinusoidal: 1891 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 5145 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: 1.040 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.180 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 : 12.246 85.881 3034 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 covalent geometry : bond 0.00580 ( 8753) covalent geometry : angle 0.77546 (11901) SS BOND : bond 0.00254 ( 4) SS BOND : angle 1.75817 ( 8) hydrogen bonds : bond 0.21787 ( 432) hydrogen bonds : angle 7.94157 ( 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 : 0.336 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: 0.7305 time to fit residues: 144.1609 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 : 0.289 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 340 ASN G 18 GLN H 3 GLN H 186 GLN H 231 GLN A 331 ASN R 122 ASN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.090048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.063001 restraints weight = 20083.649| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.04 r_work: 0.2924 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8757 Z= 0.235 Angle : 0.662 10.254 11909 Z= 0.346 Chirality : 0.045 0.177 1381 Planarity : 0.005 0.055 1496 Dihedral : 4.621 24.639 1207 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.53 % Allowed : 12.44 % 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: -0.01 (0.30), residues: 283 loop : -0.42 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 160 TYR 0.014 0.002 TYR H 190 PHE 0.013 0.002 PHE B 253 TRP 0.018 0.002 TRP B 211 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 8753) covalent geometry : angle 0.66182 (11901) SS BOND : bond 0.00321 ( 4) SS BOND : angle 1.04019 ( 8) hydrogen bonds : bond 0.04933 ( 432) hydrogen bonds : angle 5.01833 ( 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 156 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9390 (tptp) cc_final: 0.9130 (tptp) REVERT: B 32 GLN cc_start: 0.8745 (mt0) cc_final: 0.8488 (mt0) REVERT: H 13 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8385 (mm-40) REVERT: H 180 ARG cc_start: 0.9246 (mtt-85) cc_final: 0.8986 (mtt-85) REVERT: A 205 ARG cc_start: 0.8586 (mmp80) cc_final: 0.8382 (mmp80) REVERT: A 208 ARG cc_start: 0.8454 (ttm-80) cc_final: 0.8121 (ttt90) REVERT: A 306 GLN cc_start: 0.9119 (mm110) cc_final: 0.8626 (mp10) REVERT: A 345 LYS cc_start: 0.8666 (ttmt) cc_final: 0.8411 (ttmt) REVERT: R 98 TRP cc_start: 0.7728 (t-100) cc_final: 0.7517 (t-100) REVERT: R 143 ARG cc_start: 0.6666 (mmm-85) cc_final: 0.6415 (tmt90) REVERT: R 152 MET cc_start: 0.7492 (mmp) cc_final: 0.7187 (mmt) REVERT: R 223 ARG cc_start: 0.8362 (ptp-170) cc_final: 0.8096 (ptp-170) REVERT: R 396 ARG cc_start: 0.7446 (tpt170) cc_final: 0.7201 (mtt180) REVERT: R 448 ILE cc_start: 0.7472 (pt) cc_final: 0.7234 (pp) outliers start: 23 outliers final: 9 residues processed: 147 average time/residue: 0.7816 time to fit residues: 120.3926 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 : 0.334 ------------------------------------------------------------------------------- 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: 6.9990 chunk 24 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3658 r_free = 0.3658 target = 0.090332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.063460 restraints weight = 19761.171| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.98 r_work: 0.2933 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8757 Z= 0.186 Angle : 0.604 8.964 11909 Z= 0.314 Chirality : 0.042 0.162 1381 Planarity : 0.004 0.050 1496 Dihedral : 4.404 28.076 1207 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.64 % Allowed : 16.08 % Favored : 81.28 % 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: -0.07 (0.29), residues: 293 loop : -0.33 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 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 covalent geometry : bond 0.00417 ( 8753) covalent geometry : angle 0.60427 (11901) SS BOND : bond 0.00232 ( 4) SS BOND : angle 0.75089 ( 8) hydrogen bonds : bond 0.04242 ( 432) hydrogen bonds : angle 4.62751 ( 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: 24 poor density : 126 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9327 (tptp) cc_final: 0.9102 (tptp) REVERT: B 130 GLU cc_start: 0.8788 (mp0) cc_final: 0.8517 (mp0) REVERT: G 19 LEU cc_start: 0.9721 (mm) cc_final: 0.9472 (mm) REVERT: H 13 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8407 (mm-40) REVERT: H 180 ARG cc_start: 0.9301 (mtt-85) cc_final: 0.8996 (mtt-85) REVERT: A 306 GLN cc_start: 0.9097 (mm110) cc_final: 0.8629 (mp10) REVERT: A 345 LYS cc_start: 0.8702 (ttmt) cc_final: 0.8442 (ttmt) REVERT: A 349 LYS cc_start: 0.8460 (mtmm) cc_final: 0.8246 (tptp) REVERT: R 121 MET cc_start: 0.8641 (mmm) cc_final: 0.8366 (mmp) REVERT: R 143 ARG cc_start: 0.6813 (mmm-85) cc_final: 0.6591 (mtm180) REVERT: R 152 MET cc_start: 0.7572 (mmp) cc_final: 0.7273 (mmt) REVERT: R 177 LYS cc_start: 0.7588 (pptt) cc_final: 0.7354 (pptt) REVERT: R 223 ARG cc_start: 0.8382 (ptp-170) cc_final: 0.8159 (ptp-170) REVERT: R 396 ARG cc_start: 0.7478 (tpt170) cc_final: 0.7208 (mtt180) outliers start: 24 outliers final: 9 residues processed: 139 average time/residue: 0.7625 time to fit residues: 111.3412 Evaluate side-chains 121 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 A residue 261 ASP 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: 7.9990 chunk 102 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 68 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 24 optimal weight: 0.0270 chunk 63 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3658 r_free = 0.3658 target = 0.090400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.063482 restraints weight = 20043.590| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.01 r_work: 0.2935 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8757 Z= 0.172 Angle : 0.594 7.932 11909 Z= 0.308 Chirality : 0.042 0.154 1381 Planarity : 0.004 0.047 1496 Dihedral : 4.323 29.046 1207 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.64 % Allowed : 17.73 % Favored : 79.63 % 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: 0.70 (0.25), residues: 1105 helix: 1.96 (0.27), residues: 380 sheet: -0.15 (0.29), residues: 286 loop : -0.35 (0.29), residues: 439 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 0.011 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 covalent geometry : bond 0.00387 ( 8753) covalent geometry : angle 0.59350 (11901) SS BOND : bond 0.00304 ( 4) SS BOND : angle 0.71183 ( 8) hydrogen bonds : bond 0.03895 ( 432) hydrogen bonds : angle 4.46577 ( 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 145 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9279 (tptp) cc_final: 0.9053 (tptp) REVERT: B 130 GLU cc_start: 0.8799 (mp0) cc_final: 0.8507 (mp0) REVERT: H 180 ARG cc_start: 0.9322 (mtt-85) cc_final: 0.9017 (mtt-85) REVERT: H 244 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8873 (ttpp) REVERT: A 306 GLN cc_start: 0.9096 (mm110) cc_final: 0.8694 (mp10) REVERT: A 345 LYS cc_start: 0.8687 (ttmt) cc_final: 0.8424 (ttmt) REVERT: A 349 LYS cc_start: 0.8528 (mtmm) cc_final: 0.8292 (tptp) REVERT: R 86 MET cc_start: 0.7485 (mmt) cc_final: 0.7237 (mmt) REVERT: R 98 TRP cc_start: 0.7198 (t-100) cc_final: 0.6842 (t-100) REVERT: R 143 ARG cc_start: 0.6830 (mmm-85) cc_final: 0.6522 (tmt90) REVERT: R 152 MET cc_start: 0.7685 (mmp) cc_final: 0.7367 (mmt) REVERT: R 396 ARG cc_start: 0.7458 (tpt170) cc_final: 0.7200 (mtt180) REVERT: R 452 CYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7544 (p) outliers start: 24 outliers final: 9 residues processed: 135 average time/residue: 0.7455 time to fit residues: 105.5921 Evaluate side-chains 124 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 47 ASN Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 261 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 70 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3643 r_free = 0.3643 target = 0.089577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.062629 restraints weight = 19936.566| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.98 r_work: 0.2913 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8757 Z= 0.214 Angle : 0.613 8.534 11909 Z= 0.319 Chirality : 0.043 0.154 1381 Planarity : 0.004 0.047 1496 Dihedral : 4.349 28.512 1207 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.52 % Allowed : 18.28 % Favored : 78.19 % 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: 1.98 (0.27), residues: 379 sheet: -0.12 (0.29), residues: 291 loop : -0.34 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 160 TYR 0.014 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 covalent geometry : bond 0.00488 ( 8753) covalent geometry : angle 0.61252 (11901) SS BOND : bond 0.00189 ( 4) SS BOND : angle 0.74037 ( 8) hydrogen bonds : bond 0.03991 ( 432) hydrogen bonds : angle 4.48072 ( 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 154 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9304 (tptp) cc_final: 0.9071 (tptp) REVERT: G 19 LEU cc_start: 0.9721 (mm) cc_final: 0.9512 (mm) REVERT: H 76 LYS cc_start: 0.9097 (mtmm) cc_final: 0.8793 (mtmm) REVERT: H 154 SER cc_start: 0.8876 (m) cc_final: 0.8652 (p) REVERT: H 180 ARG cc_start: 0.9351 (mtt-85) cc_final: 0.9016 (mtt-85) REVERT: H 244 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8928 (ttpp) REVERT: A 306 GLN cc_start: 0.9083 (mm110) cc_final: 0.8684 (mp10) REVERT: A 345 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8444 (ttmt) REVERT: A 349 LYS cc_start: 0.8589 (mtmm) cc_final: 0.8298 (tptp) REVERT: R 143 ARG cc_start: 0.6876 (mmm-85) cc_final: 0.6535 (tmt90) REVERT: R 152 MET cc_start: 0.7671 (mmp) cc_final: 0.7379 (mmt) REVERT: R 396 ARG cc_start: 0.7502 (tpt170) cc_final: 0.7242 (mtt180) REVERT: R 440 TRP cc_start: 0.8273 (t-100) cc_final: 0.7919 (t-100) outliers start: 32 outliers final: 13 residues processed: 142 average time/residue: 0.7315 time to fit residues: 109.0978 Evaluate side-chains 128 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 244 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 122 ASN Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 212 THR 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: 0.9980 chunk 9 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3675 r_free = 0.3675 target = 0.091445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.064735 restraints weight = 19738.044| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.96 r_work: 0.2963 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2988 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= 0.128 Angle : 0.588 9.038 11909 Z= 0.302 Chirality : 0.041 0.157 1381 Planarity : 0.004 0.049 1496 Dihedral : 4.164 30.908 1207 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.20 % Allowed : 20.48 % Favored : 77.31 % 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: 2.06 (0.27), residues: 381 sheet: -0.07 (0.29), residues: 291 loop : -0.22 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 160 TYR 0.017 0.001 TYR H 190 PHE 0.011 0.001 PHE B 199 TRP 0.022 0.002 TRP R 440 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8753) covalent geometry : angle 0.58854 (11901) SS BOND : bond 0.00208 ( 4) SS BOND : angle 0.51863 ( 8) hydrogen bonds : bond 0.03467 ( 432) hydrogen bonds : angle 4.29717 ( 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 145 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9277 (tptp) cc_final: 0.9045 (tptp) REVERT: H 76 LYS cc_start: 0.9038 (mtmm) cc_final: 0.8758 (mtmm) REVERT: H 180 ARG cc_start: 0.9400 (mtt-85) cc_final: 0.9078 (mtt-85) REVERT: H 244 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8878 (ttpp) REVERT: A 25 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7693 (tm-30) REVERT: A 306 GLN cc_start: 0.9063 (mm110) cc_final: 0.8685 (mp10) REVERT: A 345 LYS cc_start: 0.8668 (ttmt) cc_final: 0.8402 (ttmt) REVERT: A 349 LYS cc_start: 0.8601 (mtmm) cc_final: 0.8328 (tptp) REVERT: R 143 ARG cc_start: 0.6956 (mmm-85) cc_final: 0.6630 (tmt90) REVERT: R 152 MET cc_start: 0.7692 (mmp) cc_final: 0.7425 (mmt) REVERT: R 396 ARG cc_start: 0.7480 (tpt170) cc_final: 0.7234 (mtt180) outliers start: 20 outliers final: 7 residues processed: 136 average time/residue: 0.7964 time to fit residues: 113.4946 Evaluate side-chains 127 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 261 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 96 optimal weight: 0.0870 overall best weight: 1.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3668 r_free = 0.3668 target = 0.091095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.064326 restraints weight = 19956.578| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.98 r_work: 0.2955 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3070 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= 0.144 Angle : 0.609 11.586 11909 Z= 0.310 Chirality : 0.041 0.154 1381 Planarity : 0.004 0.059 1496 Dihedral : 4.158 31.398 1207 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.98 % Allowed : 21.48 % Favored : 76.54 % 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: 0.93 (0.26), residues: 1105 helix: 2.10 (0.27), residues: 375 sheet: -0.02 (0.29), residues: 303 loop : -0.15 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 223 TYR 0.016 0.001 TYR H 190 PHE 0.011 0.001 PHE B 199 TRP 0.027 0.002 TRP R 440 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8753) covalent geometry : angle 0.60923 (11901) SS BOND : bond 0.00185 ( 4) SS BOND : angle 0.54621 ( 8) hydrogen bonds : bond 0.03507 ( 432) hydrogen bonds : angle 4.27175 ( 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 138 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9275 (tptp) cc_final: 0.9042 (tptp) REVERT: B 217 MET cc_start: 0.9238 (pmm) cc_final: 0.9030 (pmm) REVERT: H 76 LYS cc_start: 0.9037 (mtmm) cc_final: 0.8758 (mtmm) REVERT: H 180 ARG cc_start: 0.9411 (mtt-85) cc_final: 0.9087 (mtt-85) REVERT: H 244 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8928 (ttpp) REVERT: A 306 GLN cc_start: 0.9069 (mm110) cc_final: 0.8696 (mp10) REVERT: A 345 LYS cc_start: 0.8668 (ttmt) cc_final: 0.8393 (ttmt) REVERT: A 349 LYS cc_start: 0.8615 (mtmm) cc_final: 0.8327 (tptp) REVERT: R 86 MET cc_start: 0.7195 (mmt) cc_final: 0.6662 (mmt) REVERT: R 143 ARG cc_start: 0.6994 (mmm-85) cc_final: 0.6652 (tmt90) REVERT: R 152 MET cc_start: 0.7697 (mmp) cc_final: 0.7440 (mmt) REVERT: R 396 ARG cc_start: 0.7486 (tpt170) cc_final: 0.7264 (mtt180) outliers start: 18 outliers final: 8 residues processed: 129 average time/residue: 0.7898 time to fit residues: 106.8634 Evaluate side-chains 126 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 244 LYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 261 ASP 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: 6.9990 chunk 24 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.088427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.061448 restraints weight = 20129.004| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.97 r_work: 0.2881 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 8757 Z= 0.306 Angle : 0.705 11.942 11909 Z= 0.364 Chirality : 0.045 0.154 1381 Planarity : 0.005 0.049 1496 Dihedral : 4.507 26.858 1207 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.19 % Allowed : 20.37 % Favored : 76.43 % 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: 0.66 (0.25), residues: 1105 helix: 1.80 (0.27), residues: 379 sheet: -0.10 (0.29), residues: 295 loop : -0.29 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 160 TYR 0.016 0.002 TYR H 227 PHE 0.015 0.002 PHE B 253 TRP 0.026 0.002 TRP R 440 HIS 0.005 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00696 ( 8753) covalent geometry : angle 0.70518 (11901) SS BOND : bond 0.00156 ( 4) SS BOND : angle 0.90317 ( 8) hydrogen bonds : bond 0.04290 ( 432) hydrogen bonds : angle 4.57125 ( 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 143 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9317 (tptp) cc_final: 0.9079 (tptp) REVERT: B 130 GLU cc_start: 0.8817 (mp0) cc_final: 0.8603 (mp0) REVERT: H 180 ARG cc_start: 0.9428 (mtt-85) cc_final: 0.9095 (mtt-85) REVERT: H 244 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8944 (ttpp) REVERT: A 306 GLN cc_start: 0.9102 (mm110) cc_final: 0.8661 (mp10) REVERT: A 345 LYS cc_start: 0.8717 (ttmt) cc_final: 0.8442 (ttmt) REVERT: A 349 LYS cc_start: 0.8697 (mtmm) cc_final: 0.8406 (tptp) REVERT: R 86 MET cc_start: 0.7163 (mmt) cc_final: 0.6568 (mmt) REVERT: R 143 ARG cc_start: 0.6910 (mmm-85) cc_final: 0.6549 (tmt170) REVERT: R 152 MET cc_start: 0.7625 (mmp) cc_final: 0.7365 (mmt) REVERT: R 223 ARG cc_start: 0.8194 (ptp90) cc_final: 0.7641 (ptp-170) REVERT: R 396 ARG cc_start: 0.7557 (tpt170) cc_final: 0.7289 (mtt180) outliers start: 29 outliers final: 18 residues processed: 133 average time/residue: 0.7358 time to fit residues: 102.9622 Evaluate side-chains 129 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain R residue 121 MET Chi-restraints excluded: chain R residue 122 ASN 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 441 LEU Chi-restraints excluded: chain R residue 444 VAL 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: 0.9980 chunk 31 optimal weight: 0.4980 chunk 70 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 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 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN H 231 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 122 ASN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.091212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.064391 restraints weight = 19915.288| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.97 r_work: 0.2951 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3200 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= 0.139 Angle : 0.652 13.063 11909 Z= 0.330 Chirality : 0.042 0.165 1381 Planarity : 0.004 0.050 1496 Dihedral : 4.270 29.811 1207 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.54 % Allowed : 22.47 % 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: 0.83 (0.26), residues: 1105 helix: 1.99 (0.27), residues: 374 sheet: -0.01 (0.30), residues: 301 loop : -0.20 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 32 TYR 0.017 0.001 TYR H 190 PHE 0.011 0.001 PHE B 199 TRP 0.027 0.001 TRP R 440 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8753) covalent geometry : angle 0.65178 (11901) SS BOND : bond 0.00225 ( 4) SS BOND : angle 0.53159 ( 8) hydrogen bonds : bond 0.03538 ( 432) hydrogen bonds : angle 4.33937 ( 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 135 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9269 (tptp) cc_final: 0.9063 (tptp) REVERT: H 180 ARG cc_start: 0.9418 (mtt-85) cc_final: 0.9099 (mtt-85) REVERT: H 244 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.8932 (ttpp) REVERT: A 25 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7649 (tm-30) REVERT: A 306 GLN cc_start: 0.9094 (mm110) cc_final: 0.8710 (mp10) REVERT: A 345 LYS cc_start: 0.8662 (ttmt) cc_final: 0.8352 (ttmt) REVERT: A 349 LYS cc_start: 0.8702 (mtmm) cc_final: 0.8378 (tptp) REVERT: R 86 MET cc_start: 0.7161 (mmt) cc_final: 0.6641 (mmt) REVERT: R 143 ARG cc_start: 0.7009 (mmm-85) cc_final: 0.6621 (tmt90) REVERT: R 152 MET cc_start: 0.7702 (mmp) cc_final: 0.7418 (mmt) REVERT: R 223 ARG cc_start: 0.8257 (ptp90) cc_final: 0.7504 (ptp-170) REVERT: R 396 ARG cc_start: 0.7513 (tpt170) cc_final: 0.7285 (mtt180) outliers start: 14 outliers final: 12 residues processed: 130 average time/residue: 0.7909 time to fit residues: 107.6425 Evaluate side-chains 131 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 12 VAL 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 A residue 261 ASP 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 39 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 3 optimal weight: 0.0270 chunk 49 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 109 optimal weight: 0.2980 chunk 9 optimal weight: 0.0010 chunk 25 optimal weight: 0.3980 overall best weight: 0.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.093536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.067021 restraints weight = 19811.976| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.98 r_work: 0.3013 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8757 Z= 0.123 Angle : 0.659 13.476 11909 Z= 0.331 Chirality : 0.042 0.172 1381 Planarity : 0.004 0.054 1496 Dihedral : 4.175 32.899 1207 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.54 % Allowed : 22.47 % 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: 0.96 (0.26), residues: 1105 helix: 2.07 (0.27), residues: 375 sheet: 0.17 (0.31), residues: 285 loop : -0.21 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 205 TYR 0.028 0.001 TYR A 296 PHE 0.009 0.001 PHE R 189 TRP 0.074 0.002 TRP R 98 HIS 0.003 0.000 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8753) covalent geometry : angle 0.65895 (11901) SS BOND : bond 0.00497 ( 4) SS BOND : angle 0.62336 ( 8) hydrogen bonds : bond 0.03208 ( 432) hydrogen bonds : angle 4.19918 ( 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 143 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 GLU cc_start: 0.8793 (mp0) cc_final: 0.8550 (mp0) REVERT: H 180 ARG cc_start: 0.9436 (mtt-85) cc_final: 0.9139 (mtt-85) REVERT: A 25 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7790 (tm-30) REVERT: A 205 ARG cc_start: 0.8865 (mmm160) cc_final: 0.8590 (mmp80) REVERT: A 306 GLN cc_start: 0.9089 (mm110) cc_final: 0.8741 (mp10) REVERT: A 318 GLU cc_start: 0.8039 (tt0) cc_final: 0.7726 (tp30) REVERT: A 345 LYS cc_start: 0.8630 (ttmt) cc_final: 0.8319 (ttmt) REVERT: A 349 LYS cc_start: 0.8691 (mtmm) cc_final: 0.8369 (tptp) REVERT: R 86 MET cc_start: 0.7026 (mmt) cc_final: 0.5951 (mtp) REVERT: R 143 ARG cc_start: 0.6942 (mmm-85) cc_final: 0.6552 (tmt170) REVERT: R 152 MET cc_start: 0.7684 (mmp) cc_final: 0.7427 (mmt) REVERT: R 177 LYS cc_start: 0.7370 (pptt) cc_final: 0.6895 (pptt) REVERT: R 223 ARG cc_start: 0.8245 (ptp90) cc_final: 0.7536 (ptp-170) REVERT: R 396 ARG cc_start: 0.7514 (tpt170) cc_final: 0.7289 (mtt180) outliers start: 14 outliers final: 10 residues processed: 139 average time/residue: 0.8014 time to fit residues: 116.7711 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 : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 219 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 21 optimal weight: 0.0070 chunk 104 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 3 optimal weight: 0.0070 overall best weight: 1.1018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.092528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.065891 restraints weight = 19871.192| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.98 r_work: 0.2989 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8757 Z= 0.138 Angle : 0.686 14.191 11909 Z= 0.342 Chirality : 0.042 0.159 1381 Planarity : 0.004 0.056 1496 Dihedral : 4.189 32.035 1207 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.76 % Allowed : 23.35 % Favored : 74.89 % 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: 0.97 (0.26), residues: 1105 helix: 2.09 (0.27), residues: 375 sheet: 0.04 (0.30), residues: 302 loop : -0.11 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 205 TYR 0.018 0.001 TYR H 190 PHE 0.019 0.001 PHE B 253 TRP 0.052 0.002 TRP R 98 HIS 0.007 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8753) covalent geometry : angle 0.68579 (11901) SS BOND : bond 0.00237 ( 4) SS BOND : angle 0.86114 ( 8) hydrogen bonds : bond 0.03347 ( 432) hydrogen bonds : angle 4.19199 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3949.00 seconds wall clock time: 67 minutes 51.36 seconds (4071.36 seconds total)