Starting phenix.real_space_refine on Sat Jun 7 07:36:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7trs_26102/06_2025/7trs_26102.cif Found real_map, /net/cci-nas-00/data/ceres_data/7trs_26102/06_2025/7trs_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_26102/06_2025/7trs_26102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7trs_26102/06_2025/7trs_26102.map" model { file = "/net/cci-nas-00/data/ceres_data/7trs_26102/06_2025/7trs_26102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7trs_26102/06_2025/7trs_26102.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 1} 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, 'GLU:plan': 2, 'ARG: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, 'GLN:plan1': 1, 'ARG:plan': 3} 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: 5.59, per 1000 atoms: 0.65 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: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.13 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: 2.69 Time building geometry restraints manager: 2.74 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: 1.100 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.400 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.570 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (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 TRP 0.026 0.002 TRP R 164 HIS 0.008 0.001 HIS B 142 PHE 0.023 0.002 PHE R 204 TYR 0.016 0.002 TYR A 302 ARG 0.006 0.001 ARG R 178 Details of bonding type rmsd hydrogen bonds : bond 0.21787 ( 432) hydrogen bonds : angle 7.94157 ( 1266) SS BOND : bond 0.00254 ( 4) SS BOND : angle 1.75817 ( 8) covalent geometry : bond 0.00580 ( 8753) covalent geometry : angle 0.77546 (11901) *********************** 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 : 0.964 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: 0.8315 (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: 1.5004 time to fit residues: 297.3227 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 : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.0980 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.091850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.064987 restraints weight = 19597.796| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.04 r_work: 0.2966 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2036 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= 0.161 Angle : 0.625 9.754 11909 Z= 0.324 Chirality : 0.043 0.178 1381 Planarity : 0.005 0.055 1496 Dihedral : 4.470 25.146 1207 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.53 % Allowed : 11.45 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.25), residues: 1105 helix: 0.98 (0.26), residues: 381 sheet: 0.03 (0.29), residues: 291 loop : -0.40 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 PHE 0.013 0.001 PHE B 253 TYR 0.015 0.001 TYR H 190 ARG 0.006 0.001 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.04635 ( 432) hydrogen bonds : angle 4.96412 ( 1266) SS BOND : bond 0.00311 ( 4) SS BOND : angle 0.90050 ( 8) covalent geometry : bond 0.00354 ( 8753) covalent geometry : angle 0.62475 (11901) *********************** 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 162 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 ASN cc_start: 0.9134 (m-40) cc_final: 0.8929 (m-40) REVERT: B 23 LYS cc_start: 0.9386 (tptp) cc_final: 0.9112 (tptp) REVERT: B 32 GLN cc_start: 0.8739 (mt0) cc_final: 0.8481 (mt0) REVERT: H 13 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8402 (mm-40) REVERT: H 180 ARG cc_start: 0.9203 (mtt-85) cc_final: 0.8966 (mtt-85) REVERT: A 306 GLN cc_start: 0.9113 (mm110) cc_final: 0.8668 (mp10) REVERT: A 345 LYS cc_start: 0.8635 (ttmt) cc_final: 0.8421 (ttmt) REVERT: R 143 ARG cc_start: 0.6651 (mmm-85) cc_final: 0.6413 (tmt90) REVERT: R 152 MET cc_start: 0.7504 (mmp) cc_final: 0.7192 (mmt) REVERT: R 177 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7470 (pptt) REVERT: R 223 ARG cc_start: 0.8335 (ptp-170) cc_final: 0.8099 (ptp-170) REVERT: R 396 ARG cc_start: 0.7425 (tpt170) cc_final: 0.7166 (mtt180) outliers start: 23 outliers final: 7 residues processed: 152 average time/residue: 1.5704 time to fit residues: 251.4941 Evaluate side-chains 131 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 177 LYS 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 106 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 30.0000 chunk 90 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 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 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN H 231 GLN 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 = 0.3623 r_free = 0.3623 target = 0.088526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.061669 restraints weight = 20202.903| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.00 r_work: 0.2889 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 8757 Z= 0.313 Angle : 0.682 8.976 11909 Z= 0.357 Chirality : 0.045 0.161 1381 Planarity : 0.005 0.048 1496 Dihedral : 4.590 25.436 1207 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.86 % Allowed : 16.30 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1105 helix: 1.58 (0.26), residues: 380 sheet: -0.16 (0.29), residues: 295 loop : -0.38 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 98 HIS 0.005 0.002 HIS B 142 PHE 0.017 0.002 PHE B 253 TYR 0.017 0.002 TYR H 227 ARG 0.006 0.001 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.04760 ( 432) hydrogen bonds : angle 4.79516 ( 1266) SS BOND : bond 0.00312 ( 4) SS BOND : angle 1.14680 ( 8) covalent geometry : bond 0.00706 ( 8753) covalent geometry : angle 0.68160 (11901) *********************** 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 148 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9365 (tptp) cc_final: 0.9146 (tptp) REVERT: B 130 GLU cc_start: 0.8792 (mp0) cc_final: 0.8511 (mp0) REVERT: G 19 LEU cc_start: 0.9722 (mm) cc_final: 0.9496 (mm) REVERT: H 13 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8337 (mm-40) REVERT: H 73 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7923 (t0) REVERT: H 76 LYS cc_start: 0.9132 (mtmm) cc_final: 0.8808 (mtmm) REVERT: H 154 SER cc_start: 0.8851 (m) cc_final: 0.8618 (p) REVERT: H 180 ARG cc_start: 0.9320 (mtt-85) cc_final: 0.8998 (mtt-85) REVERT: H 244 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8821 (ttpp) REVERT: A 306 GLN cc_start: 0.9128 (mm110) cc_final: 0.8637 (mp10) REVERT: A 345 LYS cc_start: 0.8747 (ttmt) cc_final: 0.8487 (ttpt) REVERT: A 349 LYS cc_start: 0.8469 (mtmm) cc_final: 0.8248 (tptp) REVERT: R 98 TRP cc_start: 0.7144 (t-100) cc_final: 0.6716 (t-100) REVERT: R 143 ARG cc_start: 0.6807 (mmm-85) cc_final: 0.6592 (mtm180) REVERT: R 152 MET cc_start: 0.7546 (mmp) cc_final: 0.7222 (mmt) REVERT: R 177 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7483 (pptt) REVERT: R 223 ARG cc_start: 0.8394 (ptp-170) cc_final: 0.8157 (ptp-170) REVERT: R 396 ARG cc_start: 0.7511 (tpt170) cc_final: 0.7238 (mtt180) outliers start: 26 outliers final: 14 residues processed: 137 average time/residue: 1.4739 time to fit residues: 212.8680 Evaluate side-chains 127 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 73 ASP 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 129 ASP Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 437 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 444 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 68 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN H 186 GLN H 231 GLN R 122 ASN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.091820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.065012 restraints weight = 19566.026| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.99 r_work: 0.2971 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2672 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= 0.117 Angle : 0.563 8.237 11909 Z= 0.291 Chirality : 0.041 0.154 1381 Planarity : 0.004 0.049 1496 Dihedral : 4.242 29.513 1207 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.86 % Allowed : 16.19 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.25), residues: 1105 helix: 1.95 (0.27), residues: 380 sheet: -0.02 (0.30), residues: 277 loop : -0.40 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 440 HIS 0.003 0.001 HIS B 225 PHE 0.012 0.001 PHE R 84 TYR 0.017 0.001 TYR H 190 ARG 0.007 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 432) hydrogen bonds : angle 4.41231 ( 1266) SS BOND : bond 0.00236 ( 4) SS BOND : angle 0.48463 ( 8) covalent geometry : bond 0.00259 ( 8753) covalent geometry : angle 0.56292 (11901) *********************** 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 150 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9277 (tptp) cc_final: 0.9050 (tptp) REVERT: B 130 GLU cc_start: 0.8789 (mp0) cc_final: 0.8512 (mp0) REVERT: H 13 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8389 (mm-40) REVERT: H 180 ARG cc_start: 0.9291 (mtt-85) cc_final: 0.9006 (mtt-85) REVERT: H 244 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8808 (ttpp) REVERT: A 306 GLN cc_start: 0.9081 (mm110) cc_final: 0.8661 (mp10) REVERT: A 345 LYS cc_start: 0.8658 (ttmt) cc_final: 0.8399 (ttmt) REVERT: A 349 LYS cc_start: 0.8491 (mtmm) cc_final: 0.8273 (tptp) REVERT: R 86 MET cc_start: 0.7485 (mmt) cc_final: 0.7281 (mmt) REVERT: R 136 LYS cc_start: 0.7439 (mmmm) cc_final: 0.7150 (mmtp) REVERT: R 143 ARG cc_start: 0.6915 (mmm-85) cc_final: 0.6614 (tmt90) REVERT: R 152 MET cc_start: 0.7593 (mmp) cc_final: 0.7296 (mmt) REVERT: R 177 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7404 (pptt) REVERT: R 223 ARG cc_start: 0.8348 (ptp-170) cc_final: 0.8143 (ptp-170) REVERT: R 396 ARG cc_start: 0.7445 (tpt170) cc_final: 0.7186 (mtt180) REVERT: R 448 ILE cc_start: 0.7506 (pt) cc_final: 0.7186 (pp) REVERT: R 452 CYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7511 (p) outliers start: 26 outliers final: 7 residues processed: 140 average time/residue: 1.4942 time to fit residues: 220.6213 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 : 0.930 ------------------------------------------------------------------------------- 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 247 MET Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 177 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 0.0670 overall best weight: 2.2126 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.090423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.063544 restraints weight = 19846.185| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.98 r_work: 0.2933 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2829 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= 0.174 Angle : 0.582 8.296 11909 Z= 0.303 Chirality : 0.042 0.150 1381 Planarity : 0.004 0.047 1496 Dihedral : 4.248 29.988 1207 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.86 % Allowed : 17.73 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1105 helix: 1.96 (0.26), residues: 380 sheet: -0.10 (0.30), residues: 278 loop : -0.33 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 440 HIS 0.005 0.001 HIS B 225 PHE 0.013 0.001 PHE B 253 TYR 0.014 0.001 TYR H 190 ARG 0.007 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 432) hydrogen bonds : angle 4.37249 ( 1266) SS BOND : bond 0.00242 ( 4) SS BOND : angle 0.66039 ( 8) covalent geometry : bond 0.00395 ( 8753) covalent geometry : angle 0.58228 (11901) *********************** 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 147 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.974 Fit side-chains REVERT: B 23 LYS cc_start: 0.9293 (tptp) cc_final: 0.9065 (tptp) REVERT: B 130 GLU cc_start: 0.8792 (mp0) cc_final: 0.8498 (mp0) REVERT: H 76 LYS cc_start: 0.9040 (mtmm) cc_final: 0.8754 (mtmm) REVERT: H 154 SER cc_start: 0.8889 (m) cc_final: 0.8663 (p) REVERT: H 180 ARG cc_start: 0.9335 (mtt-85) cc_final: 0.9011 (mtt-85) REVERT: A 306 GLN cc_start: 0.9081 (mm110) cc_final: 0.8655 (mp10) REVERT: A 345 LYS cc_start: 0.8675 (ttmt) cc_final: 0.8412 (ttmt) REVERT: A 349 LYS cc_start: 0.8577 (mtmm) cc_final: 0.8312 (tptp) REVERT: R 136 LYS cc_start: 0.7457 (mmmm) cc_final: 0.7226 (mmtm) REVERT: R 143 ARG cc_start: 0.6961 (mmm-85) cc_final: 0.6625 (tmt90) REVERT: R 152 MET cc_start: 0.7672 (mmp) cc_final: 0.7379 (mmt) REVERT: R 177 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7432 (pptt) REVERT: R 396 ARG cc_start: 0.7489 (tpt170) cc_final: 0.7232 (mtt180) REVERT: R 440 TRP cc_start: 0.8230 (t-100) cc_final: 0.7865 (t-100) REVERT: R 448 ILE cc_start: 0.7533 (pt) cc_final: 0.7180 (pp) REVERT: R 452 CYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7461 (p) outliers start: 26 outliers final: 8 residues processed: 136 average time/residue: 1.4237 time to fit residues: 204.5592 Evaluate side-chains 122 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 12 VAL 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 177 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 86 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 23 optimal weight: 0.0870 chunk 13 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- 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 ** 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 = 0.3648 r_free = 0.3648 target = 0.089949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.063157 restraints weight = 19665.292| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.94 r_work: 0.2924 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2952 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= 0.193 Angle : 0.609 10.281 11909 Z= 0.315 Chirality : 0.042 0.153 1381 Planarity : 0.004 0.047 1496 Dihedral : 4.281 29.849 1207 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.64 % Allowed : 19.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.25), residues: 1105 helix: 1.92 (0.27), residues: 380 sheet: -0.13 (0.30), residues: 284 loop : -0.29 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 440 HIS 0.004 0.001 HIS B 225 PHE 0.013 0.001 PHE B 199 TYR 0.013 0.001 TYR H 190 ARG 0.007 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 432) hydrogen bonds : angle 4.40392 ( 1266) SS BOND : bond 0.00200 ( 4) SS BOND : angle 0.68784 ( 8) covalent geometry : bond 0.00440 ( 8753) covalent geometry : angle 0.60900 (11901) *********************** 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 143 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9296 (tptp) cc_final: 0.9067 (tptp) REVERT: H 154 SER cc_start: 0.8881 (m) cc_final: 0.8678 (p) REVERT: H 180 ARG cc_start: 0.9398 (mtt-85) cc_final: 0.9062 (mtt-85) REVERT: A 306 GLN cc_start: 0.9098 (mm110) cc_final: 0.8695 (mp10) REVERT: A 345 LYS cc_start: 0.8711 (ttmt) cc_final: 0.8441 (ttmt) REVERT: A 349 LYS cc_start: 0.8619 (mtmm) cc_final: 0.8328 (tptp) REVERT: R 136 LYS cc_start: 0.7505 (mmmm) cc_final: 0.7294 (mmtm) REVERT: R 143 ARG cc_start: 0.6902 (mmm-85) cc_final: 0.6558 (tmt90) REVERT: R 152 MET cc_start: 0.7675 (mmp) cc_final: 0.7402 (mmt) REVERT: R 396 ARG cc_start: 0.7534 (tpt170) cc_final: 0.7264 (mtt180) outliers start: 24 outliers final: 12 residues processed: 133 average time/residue: 1.5196 time to fit residues: 212.8084 Evaluate side-chains 123 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 155 VAL 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 168 ILE Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 413 TRP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.090055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.063161 restraints weight = 19969.758| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.98 r_work: 0.2925 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3048 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= 0.173 Angle : 0.615 11.721 11909 Z= 0.316 Chirality : 0.042 0.154 1381 Planarity : 0.004 0.050 1496 Dihedral : 4.246 30.326 1207 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.98 % Allowed : 20.93 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.25), residues: 1105 helix: 1.94 (0.27), residues: 380 sheet: -0.08 (0.30), residues: 285 loop : -0.22 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 440 HIS 0.004 0.001 HIS B 225 PHE 0.012 0.001 PHE B 199 TYR 0.014 0.001 TYR H 190 ARG 0.008 0.001 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 432) hydrogen bonds : angle 4.37184 ( 1266) SS BOND : bond 0.00192 ( 4) SS BOND : angle 0.62369 ( 8) covalent geometry : bond 0.00395 ( 8753) covalent geometry : angle 0.61527 (11901) *********************** 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 135 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9293 (tptp) cc_final: 0.9063 (tptp) REVERT: H 76 LYS cc_start: 0.9047 (mtmm) cc_final: 0.8768 (mtmm) REVERT: H 180 ARG cc_start: 0.9409 (mtt-85) cc_final: 0.9074 (mtt-85) REVERT: A 32 ARG cc_start: 0.8141 (ptm-80) cc_final: 0.7795 (ptm-80) REVERT: A 306 GLN cc_start: 0.9096 (mm110) cc_final: 0.8719 (mp10) REVERT: A 345 LYS cc_start: 0.8702 (ttmt) cc_final: 0.8432 (ttmt) REVERT: A 349 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8319 (tptp) REVERT: R 136 LYS cc_start: 0.7495 (mmmm) cc_final: 0.7259 (mmtm) REVERT: R 143 ARG cc_start: 0.6895 (mmm-85) cc_final: 0.6557 (tmt90) REVERT: R 152 MET cc_start: 0.7702 (mmp) cc_final: 0.7441 (mmt) REVERT: R 177 LYS cc_start: 0.7926 (pmtt) cc_final: 0.7596 (pptt) REVERT: R 396 ARG cc_start: 0.7472 (tpt170) cc_final: 0.7227 (mtt180) outliers start: 18 outliers final: 14 residues processed: 131 average time/residue: 1.5504 time to fit residues: 215.0565 Evaluate side-chains 124 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 199 VAL 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 168 ILE Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 413 TRP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 105 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.090313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.063228 restraints weight = 20170.855| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.02 r_work: 0.2923 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8757 Z= 0.173 Angle : 0.632 12.321 11909 Z= 0.322 Chirality : 0.042 0.161 1381 Planarity : 0.004 0.051 1496 Dihedral : 4.240 30.503 1207 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.98 % Allowed : 21.15 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.25), residues: 1105 helix: 1.90 (0.27), residues: 382 sheet: -0.02 (0.30), residues: 289 loop : -0.13 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 440 HIS 0.004 0.001 HIS B 225 PHE 0.012 0.001 PHE B 199 TYR 0.014 0.001 TYR H 190 ARG 0.008 0.001 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 432) hydrogen bonds : angle 4.34856 ( 1266) SS BOND : bond 0.00190 ( 4) SS BOND : angle 0.64517 ( 8) covalent geometry : bond 0.00395 ( 8753) covalent geometry : angle 0.63187 (11901) *********************** 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 133 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9275 (tptp) cc_final: 0.9049 (tptp) REVERT: B 130 GLU cc_start: 0.8778 (mp0) cc_final: 0.8551 (mp0) REVERT: H 76 LYS cc_start: 0.9051 (mtmm) cc_final: 0.8774 (mtmm) REVERT: H 180 ARG cc_start: 0.9430 (mtt-85) cc_final: 0.9115 (mtt-85) REVERT: A 306 GLN cc_start: 0.9094 (mm110) cc_final: 0.8713 (mp10) REVERT: A 345 LYS cc_start: 0.8694 (ttmt) cc_final: 0.8420 (ttmt) REVERT: A 349 LYS cc_start: 0.8684 (mtmm) cc_final: 0.8358 (tptp) REVERT: R 143 ARG cc_start: 0.6991 (mmm-85) cc_final: 0.6636 (tmt90) REVERT: R 152 MET cc_start: 0.7716 (mmp) cc_final: 0.7479 (mmt) REVERT: R 177 LYS cc_start: 0.7958 (pmtt) cc_final: 0.7618 (pptt) REVERT: R 396 ARG cc_start: 0.7510 (tpt170) cc_final: 0.7263 (mtt180) outliers start: 18 outliers final: 14 residues processed: 129 average time/residue: 1.5513 time to fit residues: 210.8764 Evaluate side-chains 123 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL 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 199 VAL 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 413 TRP 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 77 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.089914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.062886 restraints weight = 20070.310| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.00 r_work: 0.2915 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8757 Z= 0.196 Angle : 0.669 12.618 11909 Z= 0.341 Chirality : 0.043 0.189 1381 Planarity : 0.005 0.062 1496 Dihedral : 4.308 29.822 1207 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.09 % Allowed : 21.15 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1105 helix: 1.91 (0.27), residues: 380 sheet: -0.02 (0.30), residues: 289 loop : -0.14 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 440 HIS 0.004 0.001 HIS B 225 PHE 0.012 0.001 PHE B 253 TYR 0.024 0.002 TYR A 296 ARG 0.017 0.001 ARG R 223 Details of bonding type rmsd hydrogen bonds : bond 0.03793 ( 432) hydrogen bonds : angle 4.36739 ( 1266) SS BOND : bond 0.00183 ( 4) SS BOND : angle 0.69564 ( 8) covalent geometry : bond 0.00450 ( 8753) covalent geometry : angle 0.66895 (11901) *********************** 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 133 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9283 (tptp) cc_final: 0.9049 (tptp) REVERT: B 130 GLU cc_start: 0.8791 (mp0) cc_final: 0.8564 (mp0) REVERT: H 76 LYS cc_start: 0.9051 (mtmm) cc_final: 0.8777 (mtmm) REVERT: H 180 ARG cc_start: 0.9435 (mtt-85) cc_final: 0.9118 (mtt-85) REVERT: A 20 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8225 (m-30) REVERT: A 306 GLN cc_start: 0.9098 (mm110) cc_final: 0.8722 (mp10) REVERT: A 345 LYS cc_start: 0.8698 (ttmt) cc_final: 0.8422 (ttmt) REVERT: A 349 LYS cc_start: 0.8691 (mtmm) cc_final: 0.8361 (tptp) REVERT: R 143 ARG cc_start: 0.7003 (mmm-85) cc_final: 0.6645 (tmt90) REVERT: R 152 MET cc_start: 0.7720 (mmp) cc_final: 0.7435 (mmt) REVERT: R 177 LYS cc_start: 0.7977 (pmtt) cc_final: 0.7624 (pptt) REVERT: R 223 ARG cc_start: 0.8328 (ptp-110) cc_final: 0.7731 (ptp-170) REVERT: R 396 ARG cc_start: 0.7529 (tpt170) cc_final: 0.7293 (mtt180) outliers start: 19 outliers final: 15 residues processed: 129 average time/residue: 1.5283 time to fit residues: 207.4532 Evaluate side-chains 127 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 199 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain R residue 45 VAL 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 441 LEU 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 61 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 66 optimal weight: 0.0370 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 94 optimal weight: 0.1980 chunk 12 optimal weight: 0.0670 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 overall best weight: 0.2596 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.093461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.066912 restraints weight = 19754.146| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.99 r_work: 0.3007 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8757 Z= 0.122 Angle : 0.653 13.380 11909 Z= 0.329 Chirality : 0.041 0.177 1381 Planarity : 0.005 0.059 1496 Dihedral : 4.164 33.534 1207 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.54 % Allowed : 22.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 1105 helix: 2.07 (0.28), residues: 374 sheet: 0.08 (0.30), residues: 287 loop : -0.08 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP R 98 HIS 0.003 0.000 HIS B 225 PHE 0.011 0.001 PHE R 189 TYR 0.017 0.001 TYR H 190 ARG 0.014 0.001 ARG R 223 Details of bonding type rmsd hydrogen bonds : bond 0.03178 ( 432) hydrogen bonds : angle 4.20468 ( 1266) SS BOND : bond 0.00333 ( 4) SS BOND : angle 1.03239 ( 8) covalent geometry : bond 0.00286 ( 8753) covalent geometry : angle 0.65265 (11901) ********************** 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 144 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: B 130 GLU cc_start: 0.8779 (mp0) cc_final: 0.8549 (mp0) REVERT: H 76 LYS cc_start: 0.8962 (mtmm) cc_final: 0.8725 (mtmm) REVERT: H 180 ARG cc_start: 0.9431 (mtt-85) cc_final: 0.9117 (mtt-85) REVERT: A 20 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8149 (m-30) REVERT: A 32 ARG cc_start: 0.8164 (ptm-80) cc_final: 0.7936 (ptm-80) REVERT: A 306 GLN cc_start: 0.9072 (mm110) cc_final: 0.8755 (mp10) REVERT: A 345 LYS cc_start: 0.8632 (ttmt) cc_final: 0.8322 (ttmt) REVERT: A 349 LYS cc_start: 0.8674 (mtmm) cc_final: 0.8370 (tptp) REVERT: R 86 MET cc_start: 0.6877 (mmt) cc_final: 0.5825 (mtp) REVERT: R 143 ARG cc_start: 0.6910 (mmm-85) cc_final: 0.6566 (tmt90) REVERT: R 152 MET cc_start: 0.7686 (mmp) cc_final: 0.7434 (mmt) REVERT: R 177 LYS cc_start: 0.7887 (pmtt) cc_final: 0.7450 (pptt) REVERT: R 223 ARG cc_start: 0.8303 (ptp-110) cc_final: 0.7802 (ptp-170) REVERT: R 396 ARG cc_start: 0.7554 (tpt170) cc_final: 0.7329 (mtt180) outliers start: 14 outliers final: 9 residues processed: 140 average time/residue: 1.5126 time to fit residues: 222.8329 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 : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL 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 20 ASP Chi-restraints excluded: chain A residue 261 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 27 optimal weight: 0.5980 chunk 88 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 105 optimal weight: 0.0470 chunk 102 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 68 optimal weight: 0.0570 chunk 66 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN H 186 GLN H 231 GLN ** A 331 ASN ** 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 = 0.3700 r_free = 0.3700 target = 0.092747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.066240 restraints weight = 19934.005| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.99 r_work: 0.2995 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3347 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= 0.132 Angle : 0.687 13.843 11909 Z= 0.341 Chirality : 0.041 0.159 1381 Planarity : 0.005 0.061 1496 Dihedral : 4.098 32.926 1207 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.65 % Allowed : 23.35 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1105 helix: 2.10 (0.27), residues: 375 sheet: 0.16 (0.30), residues: 295 loop : -0.03 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP R 98 HIS 0.003 0.001 HIS B 225 PHE 0.009 0.001 PHE R 189 TYR 0.025 0.001 TYR A 296 ARG 0.014 0.001 ARG R 223 Details of bonding type rmsd hydrogen bonds : bond 0.03251 ( 432) hydrogen bonds : angle 4.17273 ( 1266) SS BOND : bond 0.00231 ( 4) SS BOND : angle 0.73835 ( 8) covalent geometry : bond 0.00312 ( 8753) covalent geometry : angle 0.68740 (11901) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7929.73 seconds wall clock time: 136 minutes 13.12 seconds (8173.12 seconds total)