Starting phenix.real_space_refine on Tue Apr 29 12:16:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jzp_36750/04_2025/8jzp_36750.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzp_36750/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jzp_36750/04_2025/8jzp_36750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzp_36750/04_2025/8jzp_36750.map" model { file = "/net/cci-nas-00/data/ceres_data/8jzp_36750/04_2025/8jzp_36750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzp_36750/04_2025/8jzp_36750.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 1, 'ASP:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 7} 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: {'GLN:plan1': 1, 'ASP:plan': 10, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 2} 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: {'GLN:plan1': 7, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 9, 'GLU:plan': 6, 'ARG:plan': 6} 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, 'TYR:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} 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: {'GLU:plan': 3, 'ARG:plan': 2} 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, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 94 Time building chain proxies: 6.14, per 1000 atoms: 0.71 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: 2.10 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.00 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: 2.55 Time building geometry restraints manager: 2.52 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: 2.680 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.670 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.830 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (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 TRP 0.016 0.002 TRP C 169 HIS 0.012 0.001 HIS C 225 PHE 0.016 0.002 PHE C 199 TYR 0.027 0.002 TYR A 290 ARG 0.008 0.001 ARG F 3 Details of bonding type rmsd hydrogen bonds : bond 0.18334 ( 455) hydrogen bonds : angle 7.77677 ( 1266) SS BOND : bond 0.00143 ( 6) SS BOND : angle 0.95465 ( 12) covalent geometry : bond 0.00443 ( 8799) covalent geometry : angle 0.75372 (12006) *********************** 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 : 0.880 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: 0.2417 time to fit residues: 52.8093 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 : 0.970 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 chunk 49 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 47 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 68 optimal weight: 0.6980 chunk 106 optimal weight: 10.0000 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 225 HIS ** 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 = 0.4267 r_free = 0.4267 target = 0.191021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.134226 restraints weight = 10788.196| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.94 r_work: 0.3506 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8805 Z= 0.134 Angle : 0.616 7.229 12018 Z= 0.320 Chirality : 0.042 0.142 1423 Planarity : 0.005 0.078 1533 Dihedral : 4.840 26.442 1270 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.17 % Allowed : 15.23 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.25), residues: 1175 helix: 0.67 (0.25), residues: 443 sheet: -0.89 (0.31), residues: 259 loop : -0.60 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.009 0.001 HIS C 225 PHE 0.017 0.001 PHE H 239 TYR 0.012 0.001 TYR H 190 ARG 0.004 0.000 ARG F 74 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 455) hydrogen bonds : angle 5.56244 ( 1266) SS BOND : bond 0.00152 ( 6) SS BOND : angle 0.88969 ( 12) covalent geometry : bond 0.00289 ( 8799) covalent geometry : angle 0.61557 (12006) *********************** 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 191 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: B 8 GLU cc_start: 0.5223 (pp20) cc_final: 0.4664 (mm-30) REVERT: B 48 THR cc_start: 0.7972 (m) cc_final: 0.7510 (p) REVERT: B 333 GLN cc_start: 0.8821 (tp-100) cc_final: 0.8532 (tp-100) REVERT: C 234 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: C 262 MET cc_start: 0.8426 (mmm) cc_final: 0.7338 (mpp) REVERT: F 71 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7218 (tm-30) REVERT: H 239 PHE cc_start: 0.8076 (m-80) cc_final: 0.7628 (m-10) outliers start: 26 outliers final: 14 residues processed: 183 average time/residue: 0.2166 time to fit residues: 53.4432 Evaluate side-chains 171 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 85 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN B 295 ASN C 75 GLN C 183 HIS ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.182796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.125994 restraints weight = 10999.269| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.38 r_work: 0.3363 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 8805 Z= 0.287 Angle : 0.716 9.142 12018 Z= 0.377 Chirality : 0.046 0.150 1423 Planarity : 0.005 0.075 1533 Dihedral : 5.218 27.957 1268 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.99 % Allowed : 17.54 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.24), residues: 1175 helix: 0.45 (0.25), residues: 439 sheet: -1.40 (0.30), residues: 271 loop : -0.75 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 169 HIS 0.011 0.001 HIS C 225 PHE 0.017 0.002 PHE C 199 TYR 0.020 0.002 TYR H 50 ARG 0.004 0.001 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.04460 ( 455) hydrogen bonds : angle 5.67294 ( 1266) SS BOND : bond 0.00150 ( 6) SS BOND : angle 0.95619 ( 12) covalent geometry : bond 0.00670 ( 8799) covalent geometry : angle 0.71557 (12006) *********************** 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 205 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 0.965 Fit side-chains REVERT: A 77 ASN cc_start: 0.8368 (m110) cc_final: 0.7746 (m-40) REVERT: C 234 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.7912 (m-80) REVERT: C 259 GLN cc_start: 0.7997 (pt0) cc_final: 0.7742 (pt0) REVERT: C 339 TRP cc_start: 0.7906 (m-10) cc_final: 0.7062 (m-90) REVERT: F 71 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7342 (tm-30) REVERT: H 50 TYR cc_start: 0.8032 (OUTLIER) cc_final: 0.7674 (t80) REVERT: H 93 MET cc_start: 0.7855 (ttt) cc_final: 0.7600 (ttt) REVERT: H 172 THR cc_start: 0.7776 (p) cc_final: 0.7489 (p) REVERT: H 239 PHE cc_start: 0.8329 (m-80) cc_final: 0.7831 (m-10) outliers start: 41 outliers final: 25 residues processed: 192 average time/residue: 0.2188 time to fit residues: 56.6418 Evaluate side-chains 177 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 260 VAL Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 199 LEU 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 80 ILE 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 F residue 70 VAL Chi-restraints excluded: chain H residue 35 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 112 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 6 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN C 75 GLN C 175 GLN C 183 HIS ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.188716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.131802 restraints weight = 10769.394| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.97 r_work: 0.3473 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8805 Z= 0.143 Angle : 0.618 13.275 12018 Z= 0.317 Chirality : 0.042 0.144 1423 Planarity : 0.005 0.075 1533 Dihedral : 4.764 28.394 1268 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.02 % Allowed : 20.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.25), residues: 1175 helix: 0.80 (0.25), residues: 436 sheet: -1.30 (0.30), residues: 275 loop : -0.75 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 211 HIS 0.007 0.001 HIS C 225 PHE 0.015 0.001 PHE C 222 TYR 0.017 0.002 TYR A 300 ARG 0.005 0.000 ARG F 3 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 455) hydrogen bonds : angle 5.21152 ( 1266) SS BOND : bond 0.00163 ( 6) SS BOND : angle 0.67013 ( 12) covalent geometry : bond 0.00322 ( 8799) covalent geometry : angle 0.61829 (12006) *********************** 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 205 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 1.221 Fit side-chains REVERT: A 179 GLU cc_start: 0.5778 (tp30) cc_final: 0.5531 (tp30) REVERT: B 8 GLU cc_start: 0.4918 (pp20) cc_final: 0.4543 (mm-30) REVERT: B 48 THR cc_start: 0.8006 (m) cc_final: 0.7512 (p) REVERT: C 188 MET cc_start: 0.8005 (mtp) cc_final: 0.7597 (mtp) REVERT: C 234 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.8021 (m-80) REVERT: F 71 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7509 (tm-30) REVERT: G 27 ARG cc_start: 0.8670 (mpt180) cc_final: 0.8337 (mpt180) REVERT: H 239 PHE cc_start: 0.8185 (m-80) cc_final: 0.7869 (m-10) outliers start: 33 outliers final: 22 residues processed: 193 average time/residue: 0.3222 time to fit residues: 85.6579 Evaluate side-chains 185 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 176 VAL 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 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 98 SER 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 104 optimal weight: 0.0980 chunk 6 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN B 194 ASN C 142 HIS ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 HIS F 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.188167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.131477 restraints weight = 10750.166| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.90 r_work: 0.3477 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1759 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= 0.145 Angle : 0.609 9.286 12018 Z= 0.314 Chirality : 0.042 0.160 1423 Planarity : 0.005 0.072 1533 Dihedral : 4.635 29.358 1268 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.75 % Allowed : 20.83 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.25), residues: 1175 helix: 0.92 (0.26), residues: 437 sheet: -1.29 (0.30), residues: 277 loop : -0.66 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 211 HIS 0.006 0.001 HIS C 225 PHE 0.014 0.001 PHE A 83 TYR 0.019 0.002 TYR A 300 ARG 0.003 0.000 ARG H 18 Details of bonding type rmsd hydrogen bonds : bond 0.03438 ( 455) hydrogen bonds : angle 5.09914 ( 1266) SS BOND : bond 0.00144 ( 6) SS BOND : angle 0.64236 ( 12) covalent geometry : bond 0.00331 ( 8799) covalent geometry : angle 0.60911 (12006) *********************** 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 209 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 0.943 Fit side-chains REVERT: B 8 GLU cc_start: 0.4824 (pp20) cc_final: 0.4473 (mm-30) REVERT: B 48 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7532 (p) REVERT: C 188 MET cc_start: 0.8015 (mtp) cc_final: 0.7596 (mtp) REVERT: C 234 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.7926 (m-80) REVERT: C 262 MET cc_start: 0.8303 (mmm) cc_final: 0.7839 (mmp) REVERT: F 71 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7535 (tm-30) REVERT: H 93 MET cc_start: 0.7669 (ttt) cc_final: 0.7460 (ttt) REVERT: H 239 PHE cc_start: 0.8260 (m-80) cc_final: 0.7983 (m-10) outliers start: 39 outliers final: 26 residues processed: 196 average time/residue: 0.2248 time to fit residues: 59.3240 Evaluate side-chains 191 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 212 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 B residue 296 THR 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 86 LEU 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 44 optimal weight: 0.8980 chunk 37 optimal weight: 0.0040 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 HIS F 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.188730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.132425 restraints weight = 10647.766| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.87 r_work: 0.3488 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8805 Z= 0.142 Angle : 0.607 8.585 12018 Z= 0.313 Chirality : 0.042 0.195 1423 Planarity : 0.005 0.073 1533 Dihedral : 4.573 28.610 1268 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.63 % Allowed : 20.22 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.25), residues: 1175 helix: 1.04 (0.26), residues: 434 sheet: -1.33 (0.30), residues: 267 loop : -0.65 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.006 0.001 HIS C 225 PHE 0.013 0.001 PHE C 199 TYR 0.020 0.002 TYR A 300 ARG 0.004 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03347 ( 455) hydrogen bonds : angle 5.01949 ( 1266) SS BOND : bond 0.00154 ( 6) SS BOND : angle 0.58732 ( 12) covalent geometry : bond 0.00323 ( 8799) covalent geometry : angle 0.60721 (12006) *********************** 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 208 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 0.874 Fit side-chains REVERT: A 152 LEU cc_start: 0.6490 (OUTLIER) cc_final: 0.6186 (mp) REVERT: A 179 GLU cc_start: 0.5804 (tp30) cc_final: 0.5500 (tp30) REVERT: B 8 GLU cc_start: 0.4743 (pp20) cc_final: 0.4512 (mm-30) REVERT: B 48 THR cc_start: 0.8024 (OUTLIER) cc_final: 0.7543 (p) REVERT: B 351 CYS cc_start: 0.7333 (OUTLIER) cc_final: 0.6304 (m) REVERT: C 234 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7919 (m-80) REVERT: C 261 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8291 (mm) REVERT: C 264 TYR cc_start: 0.8232 (m-80) cc_final: 0.7999 (m-80) REVERT: F 70 VAL cc_start: 0.8751 (t) cc_final: 0.8498 (p) REVERT: F 71 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7356 (tm-30) REVERT: H 93 MET cc_start: 0.7750 (ttt) cc_final: 0.7541 (ttt) outliers start: 38 outliers final: 27 residues processed: 196 average time/residue: 0.2118 time to fit residues: 55.8792 Evaluate side-chains 191 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 80 VAL 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 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 B residue 296 THR Chi-restraints excluded: chain B residue 331 ASN 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 86 LEU Chi-restraints excluded: chain H residue 117 LEU 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 26 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 0.0060 chunk 2 optimal weight: 0.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN ** C 225 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 = 0.4244 r_free = 0.4244 target = 0.188500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135635 restraints weight = 10776.144| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 3.00 r_work: 0.3477 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2083 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= 0.145 Angle : 0.619 10.515 12018 Z= 0.318 Chirality : 0.042 0.185 1423 Planarity : 0.005 0.069 1533 Dihedral : 4.538 29.344 1268 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.38 % Allowed : 21.56 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.25), residues: 1175 helix: 1.08 (0.26), residues: 435 sheet: -1.34 (0.30), residues: 267 loop : -0.66 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 169 HIS 0.005 0.001 HIS C 225 PHE 0.015 0.001 PHE A 83 TYR 0.019 0.002 TYR B 303 ARG 0.004 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.03318 ( 455) hydrogen bonds : angle 4.99240 ( 1266) SS BOND : bond 0.00170 ( 6) SS BOND : angle 0.59430 ( 12) covalent geometry : bond 0.00331 ( 8799) covalent geometry : angle 0.61926 (12006) *********************** 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 200 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.903 Fit side-chains REVERT: A 77 ASN cc_start: 0.8485 (m110) cc_final: 0.7716 (m110) REVERT: A 152 LEU cc_start: 0.6499 (OUTLIER) cc_final: 0.6176 (mp) REVERT: A 179 GLU cc_start: 0.5820 (tp30) cc_final: 0.5423 (tp30) REVERT: A 198 ARG cc_start: 0.5968 (OUTLIER) cc_final: 0.5613 (mpt-90) REVERT: B 8 GLU cc_start: 0.4935 (pp20) cc_final: 0.4534 (mm-30) REVERT: B 48 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7540 (p) REVERT: B 351 CYS cc_start: 0.7416 (OUTLIER) cc_final: 0.6410 (m) REVERT: C 234 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.7930 (m-80) REVERT: C 261 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8279 (mm) REVERT: C 262 MET cc_start: 0.8351 (mmm) cc_final: 0.7933 (mmp) REVERT: F 71 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7793 (tp40) outliers start: 36 outliers final: 24 residues processed: 187 average time/residue: 0.2217 time to fit residues: 55.7085 Evaluate side-chains 186 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 80 VAL 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 198 ARG 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 B residue 331 ASN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 106 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN ** C 225 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 = 0.4235 r_free = 0.4235 target = 0.187539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.130412 restraints weight = 11020.594| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.99 r_work: 0.3458 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8805 Z= 0.162 Angle : 0.636 8.716 12018 Z= 0.328 Chirality : 0.043 0.189 1423 Planarity : 0.005 0.071 1533 Dihedral : 4.594 29.305 1268 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.75 % Allowed : 22.17 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.25), residues: 1175 helix: 1.04 (0.26), residues: 435 sheet: -1.29 (0.30), residues: 275 loop : -0.67 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 169 HIS 0.006 0.001 HIS C 225 PHE 0.015 0.001 PHE A 83 TYR 0.017 0.002 TYR A 300 ARG 0.004 0.000 ARG H 18 Details of bonding type rmsd hydrogen bonds : bond 0.03406 ( 455) hydrogen bonds : angle 5.02652 ( 1266) SS BOND : bond 0.00171 ( 6) SS BOND : angle 0.70265 ( 12) covalent geometry : bond 0.00375 ( 8799) covalent geometry : angle 0.63614 (12006) *********************** 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 198 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 1.059 Fit side-chains REVERT: A 77 ASN cc_start: 0.8517 (m110) cc_final: 0.8266 (m110) REVERT: A 152 LEU cc_start: 0.6497 (OUTLIER) cc_final: 0.6206 (mp) REVERT: A 179 GLU cc_start: 0.5851 (tp30) cc_final: 0.5487 (tp30) REVERT: A 198 ARG cc_start: 0.6032 (OUTLIER) cc_final: 0.5704 (mpt-90) REVERT: B 8 GLU cc_start: 0.4777 (pp20) cc_final: 0.4533 (mm-30) REVERT: B 48 THR cc_start: 0.8033 (OUTLIER) cc_final: 0.7529 (p) REVERT: B 205 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7392 (pt0) REVERT: B 351 CYS cc_start: 0.7415 (OUTLIER) cc_final: 0.6420 (m) REVERT: C 234 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7936 (m-80) REVERT: C 261 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8257 (mm) REVERT: F 62 ARG cc_start: 0.7891 (ptp-170) cc_final: 0.7684 (ptp-170) REVERT: F 71 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7337 (tm-30) REVERT: H 93 MET cc_start: 0.7673 (ttt) cc_final: 0.7375 (ttt) outliers start: 39 outliers final: 26 residues processed: 187 average time/residue: 0.2193 time to fit residues: 55.0981 Evaluate side-chains 185 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 80 VAL 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 198 ARG Chi-restraints excluded: chain A residue 212 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 B residue 296 THR Chi-restraints excluded: chain B residue 331 ASN 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 123 ILE Chi-restraints excluded: chain C residue 181 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 86 LEU 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 31 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 95 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 62 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 71 optimal weight: 0.2980 chunk 111 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN C 119 ASN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.188859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.144473 restraints weight = 10868.540| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 3.73 r_work: 0.3438 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2231 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= 0.142 Angle : 0.632 11.393 12018 Z= 0.324 Chirality : 0.042 0.202 1423 Planarity : 0.005 0.068 1533 Dihedral : 4.532 28.870 1268 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.26 % Allowed : 21.92 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.25), residues: 1175 helix: 1.11 (0.26), residues: 434 sheet: -1.26 (0.31), residues: 265 loop : -0.68 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 211 HIS 0.005 0.001 HIS C 225 PHE 0.012 0.001 PHE C 199 TYR 0.017 0.002 TYR H 173 ARG 0.004 0.000 ARG H 18 Details of bonding type rmsd hydrogen bonds : bond 0.03283 ( 455) hydrogen bonds : angle 4.94695 ( 1266) SS BOND : bond 0.00147 ( 6) SS BOND : angle 0.67121 ( 12) covalent geometry : bond 0.00326 ( 8799) covalent geometry : angle 0.63216 (12006) *********************** 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 194 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.903 Fit side-chains REVERT: A 77 ASN cc_start: 0.8502 (m110) cc_final: 0.7714 (m110) REVERT: A 152 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6383 (mp) REVERT: A 198 ARG cc_start: 0.6136 (OUTLIER) cc_final: 0.5776 (mpt-90) REVERT: B 8 GLU cc_start: 0.4838 (pp20) cc_final: 0.4628 (mm-30) REVERT: B 48 THR cc_start: 0.8044 (OUTLIER) cc_final: 0.7521 (p) REVERT: B 205 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7388 (pt0) REVERT: B 351 CYS cc_start: 0.7502 (OUTLIER) cc_final: 0.6546 (m) REVERT: C 234 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8165 (m-80) REVERT: C 327 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8476 (m) REVERT: F 71 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7870 (tp40) REVERT: H 93 MET cc_start: 0.7588 (ttt) cc_final: 0.7344 (ttt) REVERT: H 239 PHE cc_start: 0.8187 (m-80) cc_final: 0.7924 (m-10) outliers start: 35 outliers final: 23 residues processed: 180 average time/residue: 0.2272 time to fit residues: 54.9948 Evaluate side-chains 186 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 80 VAL 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 198 ARG Chi-restraints excluded: chain A residue 212 LEU 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 181 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 75 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 82 optimal weight: 0.2980 chunk 114 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 110 optimal weight: 0.2980 chunk 13 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN ** C 225 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 = 0.4258 r_free = 0.4258 target = 0.190067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.133913 restraints weight = 10851.364| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.93 r_work: 0.3505 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2413 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= 0.130 Angle : 0.636 13.197 12018 Z= 0.323 Chirality : 0.042 0.210 1423 Planarity : 0.005 0.067 1533 Dihedral : 4.461 29.522 1268 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.41 % Allowed : 23.51 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1175 helix: 1.16 (0.26), residues: 434 sheet: -1.25 (0.31), residues: 265 loop : -0.61 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.005 0.001 HIS C 225 PHE 0.018 0.001 PHE A 83 TYR 0.016 0.002 TYR A 258 ARG 0.005 0.000 ARG H 18 Details of bonding type rmsd hydrogen bonds : bond 0.03170 ( 455) hydrogen bonds : angle 4.89138 ( 1266) SS BOND : bond 0.00188 ( 6) SS BOND : angle 0.71041 ( 12) covalent geometry : bond 0.00294 ( 8799) covalent geometry : angle 0.63556 (12006) ********************** 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 192 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 1.203 Fit side-chains REVERT: A 198 ARG cc_start: 0.6094 (OUTLIER) cc_final: 0.5789 (mpt-90) REVERT: B 8 GLU cc_start: 0.4708 (pp20) cc_final: 0.4508 (mm-30) REVERT: B 48 THR cc_start: 0.8038 (OUTLIER) cc_final: 0.7520 (p) REVERT: B 205 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7367 (pt0) REVERT: B 351 CYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6392 (m) REVERT: C 234 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.8021 (m-80) REVERT: C 266 HIS cc_start: 0.8752 (OUTLIER) cc_final: 0.8064 (t-90) REVERT: C 327 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8330 (m) REVERT: F 71 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7808 (tp40) REVERT: H 239 PHE cc_start: 0.8251 (m-80) cc_final: 0.8003 (m-10) outliers start: 28 outliers final: 19 residues processed: 180 average time/residue: 0.2632 time to fit residues: 65.7959 Evaluate side-chains 182 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 212 LEU 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 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 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 266 HIS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 5 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.185331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.132292 restraints weight = 10936.497| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 3.10 r_work: 0.3419 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 8805 Z= 0.221 Angle : 0.706 12.456 12018 Z= 0.364 Chirality : 0.045 0.215 1423 Planarity : 0.005 0.067 1533 Dihedral : 4.805 30.253 1268 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.38 % Allowed : 23.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.25), residues: 1175 helix: 0.98 (0.25), residues: 434 sheet: -1.43 (0.30), residues: 272 loop : -0.77 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 169 HIS 0.007 0.001 HIS C 225 PHE 0.015 0.002 PHE C 199 TYR 0.018 0.002 TYR H 190 ARG 0.005 0.001 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 455) hydrogen bonds : angle 5.16021 ( 1266) SS BOND : bond 0.00154 ( 6) SS BOND : angle 0.72352 ( 12) covalent geometry : bond 0.00520 ( 8799) covalent geometry : angle 0.70591 (12006) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5085.61 seconds wall clock time: 89 minutes 10.87 seconds (5350.87 seconds total)