Starting phenix.real_space_refine on Fri Aug 22 23:53:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jzp_36750/08_2025/8jzp_36750.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzp_36750/08_2025/8jzp_36750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jzp_36750/08_2025/8jzp_36750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzp_36750/08_2025/8jzp_36750.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jzp_36750/08_2025/8jzp_36750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzp_36750/08_2025/8jzp_36750.map" } resolution = 3.45 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= 0.016 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 51 5.16 5 C 5493 2.51 5 N 1490 2.21 5 O 1588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8622 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2206 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 14, 'TRANS': 279} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 7, 'PHE:plan': 2, 'GLU:plan': 1, 'ASP:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1509 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 39} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 2, 'ASP:plan': 10, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 85 Chain: "C" Number of atoms: 2419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2419 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 232 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 7, 'ARG:plan': 6, 'ASP:plan': 9, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 121 Chain: "F" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 492 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 66} Chain breaks: 2 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'TYR:plan': 2, 'ARG:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 58 Chain: "G" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 381 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1615 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 7, 'ASP:plan': 3, 'PHE:plan': 2, 'ARG:plan': 4, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 94 Time building chain proxies: 2.45, per 1000 atoms: 0.28 Number of scatterers: 8622 At special positions: 0 Unit cell: (84.64, 123.28, 141.68, 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 51 16.00 O 1588 8.00 N 1490 7.00 C 5493 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS F 21 " - pdb=" SG CYS F 47 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 54 " distance=2.03 Simple disulfide: pdb=" SG CYS F 34 " - pdb=" SG CYS F 55 " distance=2.03 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=2.03 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: 0.87 Conformation dependent library (CDL) restraints added in 519.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2238 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 16 sheets defined 41.1% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 36 through 53 Processing helix chain 'A' and resid 54 through 64 removed outlier: 3.551A pdb=" N VAL A 59 " --> pdb=" O ASN A 55 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 87 removed outlier: 4.310A pdb=" N TRP A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 98 Processing helix chain 'A' and resid 105 through 140 Proline residue: A 113 - end of helix Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.930A pdb=" N ASN A 146 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 174 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 198 through 232 removed outlier: 5.512A pdb=" N TRP A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Proline residue: A 214 - end of helix removed outlier: 3.813A pdb=" N CYS A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 268 removed outlier: 4.053A pdb=" N LYS A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 271 through 304 removed outlier: 4.000A pdb=" N PHE A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N SER A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 4.004A pdb=" N TYR A 300 " --> pdb=" O ASN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 314 removed outlier: 4.089A pdb=" N ARG A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 32 removed outlier: 3.967A pdb=" N ALA B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.676A pdb=" N MET B 53 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 205 removed outlier: 4.074A pdb=" N GLN B 205 " --> pdb=" O VAL B 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 202 through 205' Processing helix chain 'B' and resid 208 through 217 removed outlier: 4.595A pdb=" N ILE B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N HIS B 214 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 256 removed outlier: 3.842A pdb=" N ASN B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 282 removed outlier: 3.564A pdb=" N PHE B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.527A pdb=" N ILE B 286 " --> pdb=" O PRO B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 310 removed outlier: 3.551A pdb=" N ALA B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 351 removed outlier: 3.501A pdb=" N GLN B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 removed outlier: 3.724A pdb=" N GLN C 17 " --> pdb=" O GLN C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.536A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'F' and resid 2 through 11 Processing helix chain 'F' and resid 15 through 26 Processing helix chain 'F' and resid 33 through 39 removed outlier: 3.637A pdb=" N ALA F 39 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 41 No H-bonds generated for 'chain 'F' and resid 40 through 41' Processing helix chain 'F' and resid 44 through 45 No H-bonds generated for 'chain 'F' and resid 44 through 45' Processing helix chain 'F' and resid 46 through 63 removed outlier: 3.811A pdb=" N ASN F 52 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 removed outlier: 3.855A 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 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.623A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 178 Processing sheet with id=AA2, first strand: chain 'B' and resid 186 through 192 removed outlier: 6.297A pdb=" N VAL B 34 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N PHE B 200 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU B 36 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA B 221 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 225 through 227 removed outlier: 6.521A pdb=" N VAL B 226 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.555A pdb=" N ILE C 338 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.540A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 80 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 105 removed outlier: 5.992A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 146 through 153 removed outlier: 6.669A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.935A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.475A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.751A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.538A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 34 through 35 Processing sheet with id=AB5, first strand: chain 'H' and resid 97 through 99 removed outlier: 5.209A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 140 through 142 Processing sheet with id=AB7, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.601A pdb=" N VAL H 147 " --> pdb=" O GLU H 246 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY H 225 " --> pdb=" O LEU H 245 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) 455 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: 1.39 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1396 1.31 - 1.44: 2412 1.44 - 1.57: 4928 1.57 - 1.70: 0 1.70 - 1.82: 63 Bond restraints: 8799 Sorted by residual: bond pdb=" C ASN G 59 " pdb=" N PRO G 60 " ideal model delta sigma weight residual 1.333 1.368 -0.035 7.80e-03 1.64e+04 2.05e+01 bond pdb=" C PRO G 60 " pdb=" O PRO G 60 " ideal model delta sigma weight residual 1.236 1.186 0.049 1.33e-02 5.65e+03 1.37e+01 bond pdb=" N ASP A 282 " pdb=" CA ASP A 282 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.36e+00 bond pdb=" C PRO A 170 " pdb=" O PRO A 170 " ideal model delta sigma weight residual 1.237 1.208 0.029 1.16e-02 7.43e+03 6.27e+00 bond pdb=" N PRO G 60 " pdb=" CA PRO G 60 " ideal model delta sigma weight residual 1.474 1.456 0.018 7.40e-03 1.83e+04 6.17e+00 ... (remaining 8794 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 11859 2.74 - 5.48: 132 5.48 - 8.23: 12 8.23 - 10.97: 2 10.97 - 13.71: 1 Bond angle restraints: 12006 Sorted by residual: angle pdb=" C PRO G 60 " pdb=" CA PRO G 60 " pdb=" CB PRO G 60 " ideal model delta sigma weight residual 109.92 100.44 9.48 1.10e+00 8.26e-01 7.42e+01 angle pdb=" N ARG A 198 " pdb=" CA ARG A 198 " pdb=" C ARG A 198 " ideal model delta sigma weight residual 114.75 107.67 7.08 1.26e+00 6.30e-01 3.16e+01 angle pdb=" CB MET C 262 " pdb=" CG MET C 262 " pdb=" SD MET C 262 " ideal model delta sigma weight residual 112.70 126.41 -13.71 3.00e+00 1.11e-01 2.09e+01 angle pdb=" N PRO A 170 " pdb=" CA PRO A 170 " pdb=" C PRO A 170 " ideal model delta sigma weight residual 113.57 107.82 5.75 1.31e+00 5.83e-01 1.93e+01 angle pdb=" CA GLU A 179 " pdb=" CB GLU A 179 " pdb=" CG GLU A 179 " ideal model delta sigma weight residual 114.10 121.27 -7.17 2.00e+00 2.50e-01 1.28e+01 ... (remaining 12001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4674 17.96 - 35.93: 397 35.93 - 53.89: 68 53.89 - 71.85: 10 71.85 - 89.82: 7 Dihedral angle restraints: 5156 sinusoidal: 1695 harmonic: 3461 Sorted by residual: dihedral pdb=" CB CYS F 34 " pdb=" SG CYS F 34 " pdb=" SG CYS F 55 " pdb=" CB CYS F 55 " ideal model delta sinusoidal sigma weight residual 93.00 143.19 -50.19 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CA PHE A 182 " pdb=" C PHE A 182 " pdb=" N PRO A 183 " pdb=" CA PRO A 183 " ideal model delta harmonic sigma weight residual 180.00 152.35 27.65 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CB CYS F 21 " pdb=" SG CYS F 21 " pdb=" SG CYS F 47 " pdb=" CB CYS F 47 " ideal model delta sinusoidal sigma weight residual 93.00 139.79 -46.79 1 1.00e+01 1.00e-02 3.03e+01 ... (remaining 5153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1138 0.053 - 0.105: 255 0.105 - 0.158: 27 0.158 - 0.210: 2 0.210 - 0.263: 1 Chirality restraints: 1423 Sorted by residual: chirality pdb=" CG LEU A 277 " pdb=" CB LEU A 277 " pdb=" CD1 LEU A 277 " pdb=" CD2 LEU A 277 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB ILE A 169 " pdb=" CA ILE A 169 " pdb=" CG1 ILE A 169 " pdb=" CG2 ILE A 169 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.32e-01 chirality pdb=" CG LEU A 125 " pdb=" CB LEU A 125 " pdb=" CD1 LEU A 125 " pdb=" CD2 LEU A 125 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.23e-01 ... (remaining 1420 not shown) Planarity restraints: 1533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 182 " -0.056 5.00e-02 4.00e+02 8.43e-02 1.14e+01 pdb=" N PRO A 183 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO A 183 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 183 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 59 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ASN G 59 " -0.055 2.00e-02 2.50e+03 pdb=" O ASN G 59 " 0.021 2.00e-02 2.50e+03 pdb=" N PRO G 60 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 169 " -0.015 2.00e-02 2.50e+03 2.81e-02 7.89e+00 pdb=" C ILE A 169 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE A 169 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO A 170 " -0.017 2.00e-02 2.50e+03 ... (remaining 1530 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 485 2.72 - 3.27: 9233 3.27 - 3.81: 14072 3.81 - 4.36: 16549 4.36 - 4.90: 28533 Nonbonded interactions: 68872 Sorted by model distance: nonbonded pdb=" O ASN B 194 " pdb=" ND2 ASN B 194 " model vdw 2.180 3.120 nonbonded pdb=" O ASP H 223 " pdb=" OH TYR H 227 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR A 181 " pdb=" NH2 ARG F 3 " model vdw 2.244 3.120 nonbonded pdb=" OG1 THR C 184 " pdb=" OD2 ASP C 205 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR B 291 " pdb=" O PRO B 294 " model vdw 2.294 3.040 ... (remaining 68867 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: 3.710 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.040 Process input model: 10.310 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 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 : 0.004 0.049 8805 Z= 0.221 Angle : 0.754 13.712 12018 Z= 0.426 Chirality : 0.044 0.263 1423 Planarity : 0.005 0.084 1533 Dihedral : 14.156 89.818 2900 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.73 % Allowed : 18.64 % Favored : 80.63 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.64 (0.25), residues: 1175 helix: 0.41 (0.25), residues: 434 sheet: -1.00 (0.30), residues: 287 loop : -0.65 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 3 TYR 0.027 0.002 TYR A 290 PHE 0.016 0.002 PHE C 199 TRP 0.016 0.002 TRP C 169 HIS 0.012 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 8799) covalent geometry : angle 0.75372 (12006) SS BOND : bond 0.00143 ( 6) SS BOND : angle 0.95465 ( 12) hydrogen bonds : bond 0.18334 ( 455) hydrogen bonds : angle 7.77677 ( 1266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 161 time to evaluate : 0.410 Fit side-chains REVERT: A 77 ASN cc_start: 0.7682 (m-40) cc_final: 0.7476 (m110) REVERT: B 8 GLU cc_start: 0.5418 (pp20) cc_final: 0.4380 (pp20) REVERT: C 262 MET cc_start: 0.8488 (mmm) cc_final: 0.7925 (mmp) REVERT: H 172 THR cc_start: 0.7330 (p) cc_final: 0.7126 (p) outliers start: 6 outliers final: 1 residues processed: 164 average time/residue: 0.1183 time to fit residues: 25.7540 Evaluate side-chains 158 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 194 ASN C 119 ASN ** C 225 HIS ** 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 = 0.4239 r_free = 0.4239 target = 0.188020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.130613 restraints weight = 10791.164| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.96 r_work: 0.3466 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8805 Z= 0.172 Angle : 0.639 7.217 12018 Z= 0.333 Chirality : 0.043 0.138 1423 Planarity : 0.005 0.078 1533 Dihedral : 4.984 26.883 1270 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.53 % Allowed : 15.35 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.50 (0.25), residues: 1175 helix: 0.64 (0.25), residues: 438 sheet: -1.07 (0.31), residues: 262 loop : -0.67 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 191 TYR 0.016 0.002 TYR H 190 PHE 0.018 0.001 PHE H 239 TRP 0.017 0.002 TRP C 169 HIS 0.010 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 8799) covalent geometry : angle 0.63851 (12006) SS BOND : bond 0.00135 ( 6) SS BOND : angle 0.93007 ( 12) hydrogen bonds : bond 0.04199 ( 455) hydrogen bonds : angle 5.63962 ( 1266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.329 Fit side-chains REVERT: A 77 ASN cc_start: 0.7724 (m-40) cc_final: 0.7285 (m110) REVERT: B 8 GLU cc_start: 0.5159 (pp20) cc_final: 0.4082 (pp20) REVERT: B 333 GLN cc_start: 0.8816 (tp-100) cc_final: 0.8507 (tp-100) REVERT: C 234 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.8049 (m-80) REVERT: C 339 TRP cc_start: 0.7721 (m-10) cc_final: 0.7146 (m-90) REVERT: F 71 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7238 (tm-30) REVERT: H 239 PHE cc_start: 0.8129 (m-80) cc_final: 0.7697 (m-10) outliers start: 29 outliers final: 18 residues processed: 183 average time/residue: 0.1025 time to fit residues: 25.3893 Evaluate side-chains 173 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 6 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 92 optimal weight: 0.1980 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN C 75 GLN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.188983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.131874 restraints weight = 10805.575| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.98 r_work: 0.3483 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8805 Z= 0.145 Angle : 0.602 6.968 12018 Z= 0.314 Chirality : 0.042 0.143 1423 Planarity : 0.005 0.074 1533 Dihedral : 4.762 26.602 1268 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.65 % Allowed : 17.66 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.52 (0.25), residues: 1175 helix: 0.66 (0.25), residues: 442 sheet: -1.21 (0.30), residues: 261 loop : -0.62 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 18 TYR 0.016 0.001 TYR H 173 PHE 0.013 0.001 PHE C 199 TRP 0.015 0.001 TRP A 102 HIS 0.009 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8799) covalent geometry : angle 0.60128 (12006) SS BOND : bond 0.00191 ( 6) SS BOND : angle 0.82610 ( 12) hydrogen bonds : bond 0.03769 ( 455) hydrogen bonds : angle 5.30328 ( 1266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 212 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7289 (tp) REVERT: B 8 GLU cc_start: 0.4898 (pp20) cc_final: 0.4608 (mm-30) REVERT: B 48 THR cc_start: 0.8007 (m) cc_final: 0.7531 (p) REVERT: B 333 GLN cc_start: 0.8780 (tp-100) cc_final: 0.8461 (tp-100) REVERT: C 234 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.8079 (m-80) REVERT: F 71 GLN cc_start: 0.8092 (tm-30) cc_final: 0.7464 (tm-30) REVERT: H 239 PHE cc_start: 0.8208 (m-80) cc_final: 0.7813 (m-10) outliers start: 30 outliers final: 17 residues processed: 190 average time/residue: 0.1024 time to fit residues: 26.3277 Evaluate side-chains 179 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 1 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 0.1980 chunk 63 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN B 194 ASN C 75 GLN C 175 GLN ** C 225 HIS ** 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 = 0.4246 r_free = 0.4246 target = 0.188725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.132214 restraints weight = 10860.718| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.91 r_work: 0.3485 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8805 Z= 0.147 Angle : 0.595 6.742 12018 Z= 0.310 Chirality : 0.042 0.144 1423 Planarity : 0.005 0.075 1533 Dihedral : 4.656 28.067 1268 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.63 % Allowed : 18.88 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.39 (0.25), residues: 1175 helix: 0.86 (0.25), residues: 438 sheet: -1.23 (0.30), residues: 267 loop : -0.58 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 18 TYR 0.018 0.002 TYR A 300 PHE 0.015 0.001 PHE A 182 TRP 0.012 0.001 TRP C 169 HIS 0.008 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8799) covalent geometry : angle 0.59458 (12006) SS BOND : bond 0.00153 ( 6) SS BOND : angle 0.68444 ( 12) hydrogen bonds : bond 0.03539 ( 455) hydrogen bonds : angle 5.15603 ( 1266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.327 Fit side-chains REVERT: A 212 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7244 (tp) REVERT: B 8 GLU cc_start: 0.4907 (pp20) cc_final: 0.4541 (mm-30) REVERT: B 333 GLN cc_start: 0.8742 (tp-100) cc_final: 0.8418 (tp-100) REVERT: C 234 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.8037 (m-80) REVERT: C 339 TRP cc_start: 0.7682 (m-10) cc_final: 0.6911 (m-90) REVERT: F 71 GLN cc_start: 0.8058 (tm-30) cc_final: 0.7533 (tm-30) REVERT: G 27 ARG cc_start: 0.8629 (mpt180) cc_final: 0.8341 (mpt180) REVERT: H 239 PHE cc_start: 0.8244 (m-80) cc_final: 0.7880 (m-10) outliers start: 38 outliers final: 23 residues processed: 196 average time/residue: 0.1032 time to fit residues: 27.2772 Evaluate side-chains 188 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 22 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN B 295 ASN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.184320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.131280 restraints weight = 11015.898| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.92 r_work: 0.3422 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8805 Z= 0.244 Angle : 0.683 12.949 12018 Z= 0.354 Chirality : 0.044 0.145 1423 Planarity : 0.005 0.071 1533 Dihedral : 4.949 29.416 1268 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.24 % Allowed : 19.37 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.65 (0.25), residues: 1175 helix: 0.75 (0.25), residues: 436 sheet: -1.42 (0.30), residues: 277 loop : -0.78 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 18 TYR 0.020 0.002 TYR A 300 PHE 0.016 0.002 PHE C 241 TRP 0.016 0.002 TRP C 169 HIS 0.008 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00566 ( 8799) covalent geometry : angle 0.68311 (12006) SS BOND : bond 0.00125 ( 6) SS BOND : angle 0.69610 ( 12) hydrogen bonds : bond 0.03965 ( 455) hydrogen bonds : angle 5.37316 ( 1266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 0.324 Fit side-chains REVERT: A 77 ASN cc_start: 0.8595 (m110) cc_final: 0.7993 (m110) REVERT: A 179 GLU cc_start: 0.5640 (tp30) cc_final: 0.5361 (tp30) REVERT: C 188 MET cc_start: 0.8160 (mtp) cc_final: 0.7747 (mtp) REVERT: C 234 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.7995 (m-80) REVERT: C 262 MET cc_start: 0.8273 (mmm) cc_final: 0.7785 (mmp) REVERT: F 71 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7500 (tm-30) REVERT: G 27 ARG cc_start: 0.8668 (mpt180) cc_final: 0.8442 (mpt180) outliers start: 43 outliers final: 27 residues processed: 199 average time/residue: 0.0963 time to fit residues: 25.6593 Evaluate side-chains 188 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 87 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN C 183 HIS ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 HIS F 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.185639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.141668 restraints weight = 10890.501| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 3.96 r_work: 0.3380 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8805 Z= 0.199 Angle : 0.649 10.167 12018 Z= 0.338 Chirality : 0.043 0.170 1423 Planarity : 0.005 0.072 1533 Dihedral : 4.860 29.783 1268 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.63 % Allowed : 21.68 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.61 (0.25), residues: 1175 helix: 0.81 (0.25), residues: 436 sheet: -1.44 (0.30), residues: 277 loop : -0.75 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 18 TYR 0.021 0.002 TYR A 300 PHE 0.016 0.002 PHE C 199 TRP 0.013 0.002 TRP C 211 HIS 0.008 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 8799) covalent geometry : angle 0.64945 (12006) SS BOND : bond 0.00130 ( 6) SS BOND : angle 0.61187 ( 12) hydrogen bonds : bond 0.03691 ( 455) hydrogen bonds : angle 5.28097 ( 1266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8618 (m110) cc_final: 0.7979 (m110) REVERT: A 152 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.6285 (mp) REVERT: A 179 GLU cc_start: 0.5649 (tp30) cc_final: 0.5296 (tp30) REVERT: B 8 GLU cc_start: 0.5021 (pp20) cc_final: 0.4641 (mm-30) REVERT: B 351 CYS cc_start: 0.7578 (OUTLIER) cc_final: 0.6569 (m) REVERT: C 188 MET cc_start: 0.8166 (mtp) cc_final: 0.7771 (mtp) REVERT: C 234 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.8099 (m-80) REVERT: C 262 MET cc_start: 0.8338 (mmm) cc_final: 0.7864 (mmp) REVERT: F 71 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7576 (tm-30) REVERT: G 27 ARG cc_start: 0.8688 (mpt180) cc_final: 0.8452 (mpt180) outliers start: 38 outliers final: 25 residues processed: 193 average time/residue: 0.0954 time to fit residues: 25.0175 Evaluate side-chains 186 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 99 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.188062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.131021 restraints weight = 10963.261| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.94 r_work: 0.3470 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8805 Z= 0.151 Angle : 0.616 9.579 12018 Z= 0.319 Chirality : 0.042 0.159 1423 Planarity : 0.005 0.069 1533 Dihedral : 4.651 29.958 1268 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.51 % Allowed : 21.56 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.45 (0.25), residues: 1175 helix: 0.99 (0.26), residues: 435 sheet: -1.34 (0.30), residues: 275 loop : -0.72 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 18 TYR 0.019 0.002 TYR A 300 PHE 0.017 0.001 PHE A 83 TRP 0.010 0.001 TRP C 211 HIS 0.006 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8799) covalent geometry : angle 0.61597 (12006) SS BOND : bond 0.00183 ( 6) SS BOND : angle 0.59783 ( 12) hydrogen bonds : bond 0.03389 ( 455) hydrogen bonds : angle 5.08022 ( 1266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 ILE cc_start: 0.8055 (mm) cc_final: 0.7706 (mt) REVERT: A 77 ASN cc_start: 0.8493 (m110) cc_final: 0.7722 (m110) REVERT: A 152 LEU cc_start: 0.6418 (OUTLIER) cc_final: 0.6120 (mp) REVERT: A 179 GLU cc_start: 0.5625 (tp30) cc_final: 0.5294 (tp30) REVERT: A 198 ARG cc_start: 0.5982 (OUTLIER) cc_final: 0.5573 (mpt-90) REVERT: B 8 GLU cc_start: 0.4913 (pp20) cc_final: 0.4462 (mm-30) REVERT: B 48 THR cc_start: 0.8044 (OUTLIER) cc_final: 0.7552 (p) REVERT: B 351 CYS cc_start: 0.7390 (OUTLIER) cc_final: 0.6396 (m) REVERT: C 234 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.7980 (m-80) REVERT: C 261 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8287 (mm) REVERT: F 62 ARG cc_start: 0.7901 (ptp-170) cc_final: 0.7695 (ptp-170) REVERT: F 71 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7770 (tp40) REVERT: G 27 ARG cc_start: 0.8653 (mpt180) cc_final: 0.8404 (mpt180) outliers start: 37 outliers final: 27 residues processed: 192 average time/residue: 0.0890 time to fit residues: 23.1025 Evaluate side-chains 193 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.181943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.129288 restraints weight = 10966.570| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.85 r_work: 0.3401 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 8805 Z= 0.310 Angle : 0.737 9.252 12018 Z= 0.388 Chirality : 0.047 0.197 1423 Planarity : 0.006 0.072 1533 Dihedral : 5.118 30.746 1268 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 5.12 % Allowed : 21.32 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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 aren not related in a simple way. whole: -0.77 (0.25), residues: 1175 helix: 0.74 (0.25), residues: 432 sheet: -1.56 (0.30), residues: 275 loop : -0.88 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 68 TYR 0.029 0.003 TYR H 103 PHE 0.019 0.002 PHE C 241 TRP 0.018 0.002 TRP C 339 HIS 0.010 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00726 ( 8799) covalent geometry : angle 0.73668 (12006) SS BOND : bond 0.00120 ( 6) SS BOND : angle 0.63621 ( 12) hydrogen bonds : bond 0.04101 ( 455) hydrogen bonds : angle 5.50195 ( 1266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8692 (m110) cc_final: 0.8098 (m110) REVERT: A 152 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6346 (mp) REVERT: A 179 GLU cc_start: 0.5876 (tp30) cc_final: 0.5609 (tp30) REVERT: A 198 ARG cc_start: 0.6064 (OUTLIER) cc_final: 0.5764 (mpt-90) REVERT: A 242 LYS cc_start: 0.7378 (mtmt) cc_final: 0.6902 (ttmm) REVERT: B 351 CYS cc_start: 0.7596 (OUTLIER) cc_final: 0.6638 (m) REVERT: C 188 MET cc_start: 0.8196 (mtp) cc_final: 0.7788 (mtp) REVERT: C 233 CYS cc_start: 0.8176 (t) cc_final: 0.7860 (t) REVERT: C 234 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7819 (m-80) REVERT: C 261 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8302 (mm) REVERT: F 67 HIS cc_start: 0.6147 (OUTLIER) cc_final: 0.5941 (t-90) REVERT: F 71 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7319 (tm-30) REVERT: H 50 TYR cc_start: 0.8032 (OUTLIER) cc_final: 0.7647 (t80) outliers start: 42 outliers final: 33 residues processed: 199 average time/residue: 0.0896 time to fit residues: 24.3614 Evaluate side-chains 198 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain F residue 67 HIS Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.186024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.141288 restraints weight = 10798.333| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 3.67 r_work: 0.3400 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8805 Z= 0.175 Angle : 0.667 13.243 12018 Z= 0.343 Chirality : 0.043 0.221 1423 Planarity : 0.005 0.068 1533 Dihedral : 4.847 30.500 1268 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 5.12 % Allowed : 22.17 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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 aren not related in a simple way. whole: -0.60 (0.25), residues: 1175 helix: 0.93 (0.25), residues: 432 sheet: -1.43 (0.30), residues: 273 loop : -0.87 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 18 TYR 0.022 0.002 TYR A 300 PHE 0.019 0.002 PHE A 83 TRP 0.016 0.002 TRP A 102 HIS 0.006 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 8799) covalent geometry : angle 0.66689 (12006) SS BOND : bond 0.00166 ( 6) SS BOND : angle 0.58268 ( 12) hydrogen bonds : bond 0.03571 ( 455) hydrogen bonds : angle 5.28088 ( 1266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 0.312 Fit side-chains REVERT: A 77 ASN cc_start: 0.8610 (m110) cc_final: 0.8083 (m110) REVERT: A 152 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.6385 (mp) REVERT: A 179 GLU cc_start: 0.5780 (tp30) cc_final: 0.5533 (tp30) REVERT: A 198 ARG cc_start: 0.6048 (OUTLIER) cc_final: 0.5705 (mpt-90) REVERT: B 351 CYS cc_start: 0.7516 (OUTLIER) cc_final: 0.6575 (m) REVERT: C 188 MET cc_start: 0.8137 (mtp) cc_final: 0.7774 (mtp) REVERT: C 233 CYS cc_start: 0.8218 (t) cc_final: 0.7937 (t) REVERT: C 234 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.7924 (m-80) REVERT: C 261 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8259 (mm) REVERT: C 262 MET cc_start: 0.8237 (tpp) cc_final: 0.7845 (mmp) REVERT: F 71 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7325 (tm-30) outliers start: 42 outliers final: 31 residues processed: 187 average time/residue: 0.0766 time to fit residues: 19.5483 Evaluate side-chains 187 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 chunk 0 optimal weight: 30.0000 chunk 76 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN C 142 HIS ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 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 = 0.4241 r_free = 0.4241 target = 0.188018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.131182 restraints weight = 10879.757| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.97 r_work: 0.3467 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8805 Z= 0.149 Angle : 0.654 11.767 12018 Z= 0.337 Chirality : 0.043 0.218 1423 Planarity : 0.005 0.070 1533 Dihedral : 4.681 29.799 1268 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 4.26 % Allowed : 23.39 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.53 (0.25), residues: 1175 helix: 0.95 (0.26), residues: 435 sheet: -1.42 (0.31), residues: 265 loop : -0.79 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 18 TYR 0.022 0.002 TYR A 300 PHE 0.014 0.001 PHE C 222 TRP 0.021 0.001 TRP A 102 HIS 0.005 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 8799) covalent geometry : angle 0.65404 (12006) SS BOND : bond 0.00170 ( 6) SS BOND : angle 0.59953 ( 12) hydrogen bonds : bond 0.03405 ( 455) hydrogen bonds : angle 5.12605 ( 1266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.202 Fit side-chains REVERT: A 102 TRP cc_start: 0.7306 (t-100) cc_final: 0.7018 (t-100) REVERT: A 152 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.6345 (mp) REVERT: A 179 GLU cc_start: 0.5826 (tp30) cc_final: 0.5130 (tp30) REVERT: A 198 ARG cc_start: 0.6075 (OUTLIER) cc_final: 0.5770 (mpt-90) REVERT: B 8 GLU cc_start: 0.5063 (pp20) cc_final: 0.4500 (mm-30) REVERT: B 48 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7495 (p) REVERT: B 351 CYS cc_start: 0.7352 (OUTLIER) cc_final: 0.6413 (m) REVERT: C 233 CYS cc_start: 0.8168 (t) cc_final: 0.7832 (t) REVERT: C 234 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7907 (m-80) REVERT: C 261 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8150 (mm) REVERT: C 327 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8355 (m) REVERT: F 71 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7735 (tp40) outliers start: 35 outliers final: 25 residues processed: 181 average time/residue: 0.0813 time to fit residues: 20.0170 Evaluate side-chains 181 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 0.0980 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.187525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.130622 restraints weight = 10844.668| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.95 r_work: 0.3450 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8805 Z= 0.162 Angle : 0.662 11.377 12018 Z= 0.341 Chirality : 0.043 0.211 1423 Planarity : 0.005 0.068 1533 Dihedral : 4.680 30.017 1268 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.02 % Allowed : 23.63 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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 aren not related in a simple way. whole: -0.54 (0.25), residues: 1175 helix: 0.96 (0.25), residues: 434 sheet: -1.45 (0.30), residues: 275 loop : -0.79 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 18 TYR 0.021 0.002 TYR A 300 PHE 0.021 0.002 PHE A 83 TRP 0.014 0.001 TRP A 102 HIS 0.005 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 8799) covalent geometry : angle 0.66231 (12006) SS BOND : bond 0.00168 ( 6) SS BOND : angle 0.59310 ( 12) hydrogen bonds : bond 0.03406 ( 455) hydrogen bonds : angle 5.12863 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2081.96 seconds wall clock time: 36 minutes 23.83 seconds (2183.83 seconds total)