Starting phenix.real_space_refine on Sun May 11 18:31:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ary_43798/05_2025/9ary_43798.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ary_43798/05_2025/9ary_43798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ary_43798/05_2025/9ary_43798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ary_43798/05_2025/9ary_43798.map" model { file = "/net/cci-nas-00/data/ceres_data/9ary_43798/05_2025/9ary_43798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ary_43798/05_2025/9ary_43798.cif" } resolution = 3.27 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= 0.023 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 53 5.16 5 C 5302 2.51 5 N 1424 2.21 5 O 1556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8335 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1838 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 80 Chain: "B" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1837 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2556 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 376 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1715 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 217} Chain breaks: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.25, per 1000 atoms: 0.63 Number of scatterers: 8335 At special positions: 0 Unit cell: (88.88, 123.2, 124.08, 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 53 16.00 O 1556 8.00 N 1424 7.00 C 5302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " 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: 2.00 Conformation dependent library (CDL) restraints added in 955.7 milliseconds 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2072 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 15 sheets defined 38.6% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 80 through 102 removed outlier: 3.876A pdb=" N VAL A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 106 removed outlier: 3.689A pdb=" N GLN A 106 " --> pdb=" O LYS A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 107 through 127 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 147 through 179 removed outlier: 3.513A pdb=" N TRP A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 186 removed outlier: 3.615A pdb=" N PHE A 186 " --> pdb=" O HIS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 207 removed outlier: 4.091A pdb=" N ALA A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 removed outlier: 4.440A pdb=" N VAL A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 213 " --> pdb=" O PRO A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 213' Processing helix chain 'A' and resid 217 through 221 removed outlier: 3.655A pdb=" N LYS A 220 " --> pdb=" O ASP A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 243 removed outlier: 3.892A pdb=" N ILE A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 261 removed outlier: 3.856A pdb=" N ILE A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 349 removed outlier: 3.622A pdb=" N GLN A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) Proline residue: A 338 - end of helix removed outlier: 3.596A pdb=" N VAL A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 382 removed outlier: 3.826A pdb=" N VAL A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TRP A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A 374 " --> pdb=" O TYR A 370 " (cutoff:3.500A) Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.761A pdb=" N ARG A 388 " --> pdb=" O ASN A 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 31 Processing helix chain 'B' and resid 45 through 50 removed outlier: 3.603A pdb=" N ILE B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL B 50 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 removed outlier: 3.533A pdb=" N ALA B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.533A pdb=" N LEU B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 removed outlier: 4.379A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 183 through 204 removed outlier: 3.604A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N SER B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 243 removed outlier: 3.523A pdb=" N ASP B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 removed outlier: 3.702A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.789A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN C 132 " --> pdb=" O ARG C 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 128 through 132' Processing helix chain 'D' and resid 10 through 24 removed outlier: 3.919A pdb=" N LYS D 14 " --> pdb=" O ALA D 10 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.521A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 removed outlier: 3.943A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.622A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.583A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.540A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing sheet with id=AA1, first strand: chain 'B' and resid 70 through 76 removed outlier: 7.119A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.846A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.557A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.932A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.007A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 191 removed outlier: 6.729A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 232 removed outlier: 6.737A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.507A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN C 295 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.665A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR E 115 " --> pdb=" O TYR E 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 33 through 34 Processing sheet with id=AB4, first strand: chain 'E' and resid 49 through 51 Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.694A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 143 through 148 removed outlier: 3.656A pdb=" N PHE E 200 " --> pdb=" O CYS E 147 " (cutoff:3.500A) 403 hydrogen bonds defined for protein. 1137 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: 2.27 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2702 1.34 - 1.46: 1962 1.46 - 1.58: 3764 1.58 - 1.70: 0 1.70 - 1.82: 77 Bond restraints: 8505 Sorted by residual: bond pdb=" N ASP E 189 " pdb=" CA ASP E 189 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.33e-02 5.65e+03 6.70e+00 bond pdb=" CD2 SRO A 501 " pdb=" CE2 SRO A 501 " ideal model delta sigma weight residual 1.419 1.367 0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" CD1 SRO A 501 " pdb=" NE1 SRO A 501 " ideal model delta sigma weight residual 1.377 1.327 0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" N SER C 281 " pdb=" CA SER C 281 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.33e-02 5.65e+03 6.21e+00 bond pdb=" N ARG B 32 " pdb=" CA ARG B 32 " ideal model delta sigma weight residual 1.459 1.489 -0.031 1.25e-02 6.40e+03 6.03e+00 ... (remaining 8500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 10954 1.49 - 2.99: 485 2.99 - 4.48: 85 4.48 - 5.97: 40 5.97 - 7.46: 6 Bond angle restraints: 11570 Sorted by residual: angle pdb=" CA PRO A 144 " pdb=" N PRO A 144 " pdb=" CD PRO A 144 " ideal model delta sigma weight residual 112.00 105.29 6.71 1.40e+00 5.10e-01 2.30e+01 angle pdb=" CA THR C 86 " pdb=" CB THR C 86 " pdb=" OG1 THR C 86 " ideal model delta sigma weight residual 109.60 104.67 4.93 1.50e+00 4.44e-01 1.08e+01 angle pdb=" N CYS A 337 " pdb=" CA CYS A 337 " pdb=" C CYS A 337 " ideal model delta sigma weight residual 109.81 116.95 -7.14 2.21e+00 2.05e-01 1.04e+01 angle pdb=" CA ILE C 229 " pdb=" CB ILE C 229 " pdb=" CG1 ILE C 229 " ideal model delta sigma weight residual 110.40 115.76 -5.36 1.70e+00 3.46e-01 9.94e+00 angle pdb=" CA CYS A 337 " pdb=" C CYS A 337 " pdb=" N PRO A 338 " ideal model delta sigma weight residual 118.44 123.09 -4.65 1.59e+00 3.96e-01 8.55e+00 ... (remaining 11565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4480 17.95 - 35.89: 419 35.89 - 53.84: 86 53.84 - 71.79: 14 71.79 - 89.74: 9 Dihedral angle restraints: 5008 sinusoidal: 1803 harmonic: 3205 Sorted by residual: dihedral pdb=" CB CYS A 148 " pdb=" SG CYS A 148 " pdb=" SG CYS A 227 " pdb=" CB CYS A 227 " ideal model delta sinusoidal sigma weight residual -86.00 -170.46 84.46 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CA GLU C 130 " pdb=" C GLU C 130 " pdb=" N GLY C 131 " pdb=" CA GLY C 131 " ideal model delta harmonic sigma weight residual 180.00 160.11 19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA PRO A 144 " pdb=" C PRO A 144 " pdb=" N SER A 145 " pdb=" CA SER A 145 " ideal model delta harmonic sigma weight residual -180.00 -160.49 -19.51 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 979 0.044 - 0.088: 268 0.088 - 0.132: 85 0.132 - 0.176: 14 0.176 - 0.220: 1 Chirality restraints: 1347 Sorted by residual: chirality pdb=" CB VAL A 241 " pdb=" CA VAL A 241 " pdb=" CG1 VAL A 241 " pdb=" CG2 VAL A 241 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ILE E 58 " pdb=" N ILE E 58 " pdb=" C ILE E 58 " pdb=" CB ILE E 58 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CA VAL C 327 " pdb=" N VAL C 327 " pdb=" C VAL C 327 " pdb=" CB VAL C 327 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 1344 not shown) Planarity restraints: 1471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 143 " -0.049 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO A 144 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 337 " -0.038 5.00e-02 4.00e+02 5.65e-02 5.10e+00 pdb=" N PRO A 338 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 338 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 338 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 245 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.69e+00 pdb=" N PRO A 246 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 246 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 246 " -0.031 5.00e-02 4.00e+02 ... (remaining 1468 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2125 2.80 - 3.33: 7553 3.33 - 3.85: 13113 3.85 - 4.38: 15175 4.38 - 4.90: 27369 Nonbonded interactions: 65335 Sorted by model distance: nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.278 3.040 nonbonded pdb=" O GLY C 310 " pdb=" NZ LYS C 337 " model vdw 2.279 3.120 nonbonded pdb=" OD2 ASP A 155 " pdb=" OH TYR A 370 " model vdw 2.302 3.040 nonbonded pdb=" OD1 ASN A 110 " pdb=" OH TYR A 387 " model vdw 2.306 3.040 nonbonded pdb=" OG SER C 227 " pdb=" OD1 ASP C 246 " model vdw 2.310 3.040 ... (remaining 65330 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.290 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 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 : 0.005 0.087 8508 Z= 0.220 Angle : 0.772 7.463 11576 Z= 0.425 Chirality : 0.046 0.220 1347 Planarity : 0.006 0.085 1471 Dihedral : 14.875 89.737 2927 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.12 % Allowed : 14.32 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.70 (0.24), residues: 1087 helix: 0.23 (0.26), residues: 366 sheet: -0.38 (0.31), residues: 261 loop : -0.96 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 129 HIS 0.005 0.001 HIS A 165 PHE 0.015 0.001 PHE A 244 TYR 0.014 0.002 TYR B 163 ARG 0.007 0.001 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.17835 ( 391) hydrogen bonds : angle 6.52410 ( 1137) SS BOND : bond 0.00154 ( 3) SS BOND : angle 0.74988 ( 6) covalent geometry : bond 0.00475 ( 8505) covalent geometry : angle 0.77207 (11570) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.965 Fit side-chains REVERT: A 155 ASP cc_start: 0.6920 (t0) cc_final: 0.6719 (m-30) REVERT: A 164 MET cc_start: 0.7819 (mmt) cc_final: 0.7593 (mmm) REVERT: E 211 ASP cc_start: 0.7970 (t0) cc_final: 0.7408 (t0) outliers start: 1 outliers final: 1 residues processed: 140 average time/residue: 0.2295 time to fit residues: 42.7285 Evaluate side-chains 123 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 80 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 0.0070 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 0.0870 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 317 ASN B 82 HIS C 156 GLN C 183 HIS C 239 ASN E 35 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.180812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.152037 restraints weight = 10025.737| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.39 r_work: 0.3583 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8508 Z= 0.115 Angle : 0.528 7.541 11576 Z= 0.275 Chirality : 0.041 0.133 1347 Planarity : 0.004 0.043 1471 Dihedral : 4.373 38.558 1191 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.75 % Allowed : 14.67 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.15 (0.25), residues: 1087 helix: 1.34 (0.27), residues: 359 sheet: -0.06 (0.32), residues: 260 loop : -0.73 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 339 HIS 0.003 0.001 HIS A 165 PHE 0.013 0.001 PHE E 29 TYR 0.017 0.001 TYR E 59 ARG 0.005 0.001 ARG B 208 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 391) hydrogen bonds : angle 4.31190 ( 1137) SS BOND : bond 0.00049 ( 3) SS BOND : angle 0.54714 ( 6) covalent geometry : bond 0.00259 ( 8505) covalent geometry : angle 0.52845 (11570) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.8115 (mmt) cc_final: 0.7886 (mmm) REVERT: B 14 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7411 (tt0) REVERT: E 87 ARG cc_start: 0.7471 (ptp-170) cc_final: 0.7171 (mtt90) REVERT: E 211 ASP cc_start: 0.8231 (t0) cc_final: 0.7611 (t0) outliers start: 15 outliers final: 8 residues processed: 148 average time/residue: 0.2185 time to fit residues: 43.7693 Evaluate side-chains 129 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 MET Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 229 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 81 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 343 ASN C 155 ASN C 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.174076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.144808 restraints weight = 10172.812| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.45 r_work: 0.3490 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8508 Z= 0.146 Angle : 0.546 8.601 11576 Z= 0.282 Chirality : 0.042 0.146 1347 Planarity : 0.003 0.034 1471 Dihedral : 4.211 30.286 1189 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.61 % Allowed : 13.74 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.39 (0.26), residues: 1087 helix: 1.75 (0.28), residues: 364 sheet: -0.15 (0.32), residues: 265 loop : -0.65 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 129 HIS 0.003 0.001 HIS C 266 PHE 0.012 0.001 PHE C 241 TYR 0.016 0.001 TYR B 115 ARG 0.005 0.001 ARG B 208 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 391) hydrogen bonds : angle 4.05117 ( 1137) SS BOND : bond 0.00130 ( 3) SS BOND : angle 0.68637 ( 6) covalent geometry : bond 0.00337 ( 8505) covalent geometry : angle 0.54576 (11570) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.7990 (mmt) cc_final: 0.7777 (mmm) REVERT: B 14 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7681 (tt0) REVERT: B 188 ARG cc_start: 0.7263 (ttt180) cc_final: 0.6786 (mtm110) REVERT: B 222 GLU cc_start: 0.7487 (pp20) cc_final: 0.7286 (pm20) REVERT: C 155 ASN cc_start: 0.8237 (t0) cc_final: 0.7984 (t0) REVERT: C 336 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8429 (pp) REVERT: E 211 ASP cc_start: 0.8083 (t0) cc_final: 0.7679 (t0) outliers start: 31 outliers final: 19 residues processed: 164 average time/residue: 0.2146 time to fit residues: 47.5993 Evaluate side-chains 145 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 MET Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 162 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 71 optimal weight: 0.3980 chunk 63 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN C 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.174209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.144923 restraints weight = 10146.824| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.48 r_work: 0.3494 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8508 Z= 0.120 Angle : 0.529 10.388 11576 Z= 0.270 Chirality : 0.041 0.130 1347 Planarity : 0.003 0.033 1471 Dihedral : 4.197 38.043 1189 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.84 % Allowed : 16.88 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.54 (0.26), residues: 1087 helix: 1.82 (0.27), residues: 370 sheet: -0.00 (0.33), residues: 261 loop : -0.58 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.005 0.001 HIS B 82 PHE 0.011 0.001 PHE C 241 TYR 0.016 0.001 TYR B 115 ARG 0.005 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.03201 ( 391) hydrogen bonds : angle 3.92168 ( 1137) SS BOND : bond 0.00052 ( 3) SS BOND : angle 0.47838 ( 6) covalent geometry : bond 0.00278 ( 8505) covalent geometry : angle 0.52937 (11570) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 141 TRP cc_start: 0.5780 (OUTLIER) cc_final: 0.5352 (t60) REVERT: A 164 MET cc_start: 0.7943 (mmt) cc_final: 0.7737 (mmm) REVERT: B 14 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7777 (tt0) REVERT: B 188 ARG cc_start: 0.7277 (ttt180) cc_final: 0.6779 (mtm110) REVERT: C 155 ASN cc_start: 0.8240 (t0) cc_final: 0.8003 (t0) REVERT: E 211 ASP cc_start: 0.8113 (t0) cc_final: 0.7708 (t0) outliers start: 33 outliers final: 20 residues processed: 153 average time/residue: 0.2001 time to fit residues: 41.5716 Evaluate side-chains 140 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 MET Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 192 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.9990 chunk 85 optimal weight: 0.0000 chunk 56 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.169558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.138374 restraints weight = 10328.222| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.60 r_work: 0.3445 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8508 Z= 0.130 Angle : 0.527 9.100 11576 Z= 0.271 Chirality : 0.041 0.134 1347 Planarity : 0.003 0.032 1471 Dihedral : 4.149 36.130 1189 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.49 % Allowed : 17.11 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.26), residues: 1087 helix: 1.91 (0.27), residues: 370 sheet: -0.05 (0.32), residues: 270 loop : -0.47 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 129 HIS 0.003 0.001 HIS A 165 PHE 0.013 0.001 PHE C 241 TYR 0.012 0.001 TYR E 178 ARG 0.006 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.03198 ( 391) hydrogen bonds : angle 3.89770 ( 1137) SS BOND : bond 0.00064 ( 3) SS BOND : angle 0.47910 ( 6) covalent geometry : bond 0.00303 ( 8505) covalent geometry : angle 0.52692 (11570) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: A 141 TRP cc_start: 0.5900 (OUTLIER) cc_final: 0.5390 (t60) REVERT: A 164 MET cc_start: 0.8091 (mmt) cc_final: 0.7867 (mmm) REVERT: B 14 GLU cc_start: 0.8474 (tm-30) cc_final: 0.7928 (tt0) REVERT: B 82 HIS cc_start: 0.8138 (t70) cc_final: 0.7578 (t70) REVERT: B 188 ARG cc_start: 0.7481 (ttt180) cc_final: 0.6924 (mtm110) REVERT: C 36 ASN cc_start: 0.8800 (p0) cc_final: 0.8354 (m-40) REVERT: C 118 ASP cc_start: 0.8687 (p0) cc_final: 0.8338 (p0) REVERT: C 155 ASN cc_start: 0.8288 (t0) cc_final: 0.8042 (t0) REVERT: D 47 GLU cc_start: 0.8302 (tt0) cc_final: 0.7951 (tt0) REVERT: E 79 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6452 (pt) REVERT: E 211 ASP cc_start: 0.8212 (t0) cc_final: 0.7704 (t0) outliers start: 30 outliers final: 24 residues processed: 145 average time/residue: 0.2123 time to fit residues: 42.0790 Evaluate side-chains 148 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 MET Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 192 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 99 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** B 82 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 = 0.3937 r_free = 0.3937 target = 0.165987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.135925 restraints weight = 10450.891| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.76 r_work: 0.3405 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8508 Z= 0.169 Angle : 0.563 9.091 11576 Z= 0.292 Chirality : 0.042 0.139 1347 Planarity : 0.003 0.035 1471 Dihedral : 4.287 31.389 1189 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.73 % Allowed : 17.69 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.61 (0.26), residues: 1087 helix: 1.83 (0.27), residues: 368 sheet: -0.13 (0.33), residues: 273 loop : -0.38 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 129 HIS 0.004 0.001 HIS B 82 PHE 0.014 0.001 PHE C 241 TYR 0.021 0.002 TYR E 59 ARG 0.006 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 391) hydrogen bonds : angle 4.02026 ( 1137) SS BOND : bond 0.00073 ( 3) SS BOND : angle 0.70211 ( 6) covalent geometry : bond 0.00401 ( 8505) covalent geometry : angle 0.56276 (11570) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.887 Fit side-chains REVERT: A 164 MET cc_start: 0.8006 (mmt) cc_final: 0.7782 (mmm) REVERT: B 14 GLU cc_start: 0.8450 (tm-30) cc_final: 0.7872 (tt0) REVERT: B 28 GLU cc_start: 0.7126 (tp30) cc_final: 0.6437 (mt-10) REVERT: B 75 GLN cc_start: 0.7445 (tt0) cc_final: 0.7223 (tt0) REVERT: B 188 ARG cc_start: 0.7340 (ttt180) cc_final: 0.6703 (mtm110) REVERT: C 155 ASN cc_start: 0.8312 (t0) cc_final: 0.8062 (t0) REVERT: C 339 TRP cc_start: 0.8356 (OUTLIER) cc_final: 0.8089 (m-10) REVERT: D 47 GLU cc_start: 0.8161 (tt0) cc_final: 0.7806 (tt0) REVERT: E 79 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6698 (pt) REVERT: E 211 ASP cc_start: 0.7975 (t0) cc_final: 0.7457 (t0) outliers start: 32 outliers final: 27 residues processed: 149 average time/residue: 0.2074 time to fit residues: 42.2695 Evaluate side-chains 149 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 192 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 80 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 34 optimal weight: 0.2980 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.168439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.138071 restraints weight = 10418.439| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.65 r_work: 0.3443 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8508 Z= 0.115 Angle : 0.518 8.596 11576 Z= 0.268 Chirality : 0.040 0.130 1347 Planarity : 0.003 0.030 1471 Dihedral : 4.135 35.909 1189 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.03 % Allowed : 19.21 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.27), residues: 1087 helix: 2.04 (0.28), residues: 368 sheet: -0.17 (0.33), residues: 270 loop : -0.36 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 129 HIS 0.005 0.001 HIS B 82 PHE 0.011 0.001 PHE E 29 TYR 0.014 0.001 TYR E 59 ARG 0.008 0.000 ARG B 185 Details of bonding type rmsd hydrogen bonds : bond 0.03095 ( 391) hydrogen bonds : angle 3.85933 ( 1137) SS BOND : bond 0.00088 ( 3) SS BOND : angle 0.47293 ( 6) covalent geometry : bond 0.00266 ( 8505) covalent geometry : angle 0.51842 (11570) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.921 Fit side-chains REVERT: A 164 MET cc_start: 0.7943 (mmt) cc_final: 0.7736 (mmm) REVERT: B 14 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7866 (tt0) REVERT: B 28 GLU cc_start: 0.6989 (tp30) cc_final: 0.6297 (mt-10) REVERT: B 82 HIS cc_start: 0.8096 (t70) cc_final: 0.7731 (t70) REVERT: B 188 ARG cc_start: 0.7217 (ttt180) cc_final: 0.6903 (mtp85) REVERT: C 118 ASP cc_start: 0.8252 (p0) cc_final: 0.7888 (p0) REVERT: C 155 ASN cc_start: 0.8228 (t0) cc_final: 0.7987 (t0) REVERT: D 47 GLU cc_start: 0.8175 (tt0) cc_final: 0.7802 (tt0) REVERT: E 79 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6479 (pt) REVERT: E 211 ASP cc_start: 0.7991 (t0) cc_final: 0.7537 (t0) outliers start: 26 outliers final: 21 residues processed: 152 average time/residue: 0.1826 time to fit residues: 38.7240 Evaluate side-chains 152 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 192 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 4 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 71 optimal weight: 0.0010 chunk 8 optimal weight: 0.9980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN ** B 82 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 = 0.3951 r_free = 0.3951 target = 0.167610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.137173 restraints weight = 10539.184| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.86 r_work: 0.3421 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8508 Z= 0.126 Angle : 0.524 8.508 11576 Z= 0.271 Chirality : 0.041 0.134 1347 Planarity : 0.003 0.031 1471 Dihedral : 4.095 33.038 1189 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.26 % Allowed : 19.44 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.76 (0.27), residues: 1087 helix: 2.07 (0.28), residues: 368 sheet: -0.16 (0.33), residues: 270 loop : -0.32 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 129 HIS 0.003 0.001 HIS A 165 PHE 0.018 0.001 PHE A 234 TYR 0.016 0.001 TYR E 59 ARG 0.006 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.03143 ( 391) hydrogen bonds : angle 3.86168 ( 1137) SS BOND : bond 0.00073 ( 3) SS BOND : angle 0.57940 ( 6) covalent geometry : bond 0.00293 ( 8505) covalent geometry : angle 0.52357 (11570) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 1.022 Fit side-chains REVERT: A 164 MET cc_start: 0.7958 (mmt) cc_final: 0.7756 (mmm) REVERT: A 182 HIS cc_start: 0.7411 (OUTLIER) cc_final: 0.6757 (t-170) REVERT: B 14 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7869 (tt0) REVERT: B 28 GLU cc_start: 0.6993 (tp30) cc_final: 0.6283 (mt-10) REVERT: B 82 HIS cc_start: 0.8015 (t70) cc_final: 0.7696 (t70) REVERT: B 188 ARG cc_start: 0.7130 (ttt180) cc_final: 0.6548 (mtp85) REVERT: C 118 ASP cc_start: 0.8345 (p0) cc_final: 0.7966 (p0) REVERT: C 155 ASN cc_start: 0.8230 (t0) cc_final: 0.7971 (t0) REVERT: D 47 GLU cc_start: 0.8180 (tt0) cc_final: 0.7768 (tt0) REVERT: E 79 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6467 (pt) REVERT: E 211 ASP cc_start: 0.7938 (t0) cc_final: 0.7474 (t0) outliers start: 28 outliers final: 23 residues processed: 154 average time/residue: 0.2008 time to fit residues: 42.8365 Evaluate side-chains 152 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 182 HIS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 192 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 50 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 11 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 110 ASN ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.167668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.137365 restraints weight = 10523.981| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.79 r_work: 0.3418 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8508 Z= 0.128 Angle : 0.523 9.390 11576 Z= 0.271 Chirality : 0.041 0.133 1347 Planarity : 0.003 0.031 1471 Dihedral : 4.105 32.458 1189 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.14 % Allowed : 20.37 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.77 (0.27), residues: 1087 helix: 2.07 (0.28), residues: 368 sheet: -0.11 (0.33), residues: 265 loop : -0.35 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 129 HIS 0.005 0.001 HIS B 82 PHE 0.012 0.001 PHE E 29 TYR 0.014 0.001 TYR E 59 ARG 0.006 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.03138 ( 391) hydrogen bonds : angle 3.86884 ( 1137) SS BOND : bond 0.00076 ( 3) SS BOND : angle 0.58421 ( 6) covalent geometry : bond 0.00299 ( 8505) covalent geometry : angle 0.52306 (11570) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.908 Fit side-chains REVERT: A 114 MET cc_start: 0.7677 (ptm) cc_final: 0.6480 (tpt) REVERT: A 164 MET cc_start: 0.7975 (mmt) cc_final: 0.7765 (mmm) REVERT: A 182 HIS cc_start: 0.7398 (OUTLIER) cc_final: 0.6740 (t-170) REVERT: B 14 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7901 (tt0) REVERT: B 28 GLU cc_start: 0.7018 (tp30) cc_final: 0.6328 (mt-10) REVERT: B 75 GLN cc_start: 0.7529 (tt0) cc_final: 0.7308 (tt0) REVERT: B 82 HIS cc_start: 0.8040 (t70) cc_final: 0.7745 (t70) REVERT: B 188 ARG cc_start: 0.7131 (ttt180) cc_final: 0.6526 (mtp85) REVERT: C 75 GLN cc_start: 0.7705 (tm-30) cc_final: 0.7347 (tm-30) REVERT: C 118 ASP cc_start: 0.8358 (p0) cc_final: 0.7981 (p0) REVERT: C 155 ASN cc_start: 0.8238 (t0) cc_final: 0.7997 (t0) REVERT: E 79 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6520 (pt) REVERT: E 211 ASP cc_start: 0.7927 (t0) cc_final: 0.7467 (t0) outliers start: 27 outliers final: 22 residues processed: 146 average time/residue: 0.2023 time to fit residues: 40.7645 Evaluate side-chains 148 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 182 HIS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 192 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 44 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.0010 chunk 27 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.167974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.137881 restraints weight = 10458.687| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.80 r_work: 0.3426 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8508 Z= 0.122 Angle : 0.523 10.021 11576 Z= 0.270 Chirality : 0.041 0.132 1347 Planarity : 0.003 0.034 1471 Dihedral : 4.081 33.949 1189 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.03 % Allowed : 20.37 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.81 (0.27), residues: 1087 helix: 2.12 (0.28), residues: 368 sheet: -0.09 (0.33), residues: 265 loop : -0.33 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 129 HIS 0.005 0.001 HIS B 82 PHE 0.037 0.001 PHE A 234 TYR 0.014 0.001 TYR E 59 ARG 0.006 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 391) hydrogen bonds : angle 3.84201 ( 1137) SS BOND : bond 0.00068 ( 3) SS BOND : angle 0.53439 ( 6) covalent geometry : bond 0.00283 ( 8505) covalent geometry : angle 0.52255 (11570) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.829 Fit side-chains REVERT: A 114 MET cc_start: 0.7686 (ptm) cc_final: 0.6489 (tpt) REVERT: A 182 HIS cc_start: 0.7367 (OUTLIER) cc_final: 0.6732 (t-170) REVERT: B 14 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7934 (tt0) REVERT: B 28 GLU cc_start: 0.7053 (tp30) cc_final: 0.6375 (mt-10) REVERT: B 75 GLN cc_start: 0.7513 (tt0) cc_final: 0.7295 (tt0) REVERT: B 82 HIS cc_start: 0.8031 (t70) cc_final: 0.7746 (t70) REVERT: B 188 ARG cc_start: 0.6987 (ttt180) cc_final: 0.6367 (mtp85) REVERT: C 75 GLN cc_start: 0.7691 (tm-30) cc_final: 0.7337 (tm-30) REVERT: C 118 ASP cc_start: 0.8359 (p0) cc_final: 0.7971 (p0) REVERT: C 155 ASN cc_start: 0.8238 (t0) cc_final: 0.7986 (t0) REVERT: E 79 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6501 (pt) REVERT: E 211 ASP cc_start: 0.7915 (t0) cc_final: 0.7456 (t0) outliers start: 26 outliers final: 22 residues processed: 143 average time/residue: 0.2075 time to fit residues: 40.9284 Evaluate side-chains 149 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 182 HIS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 150 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 0.0980 chunk 94 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.169015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.139451 restraints weight = 10528.684| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.55 r_work: 0.3456 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8508 Z= 0.110 Angle : 0.513 9.747 11576 Z= 0.266 Chirality : 0.040 0.130 1347 Planarity : 0.003 0.031 1471 Dihedral : 4.012 34.530 1189 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.56 % Allowed : 20.72 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.88 (0.27), residues: 1087 helix: 2.18 (0.28), residues: 370 sheet: 0.00 (0.33), residues: 269 loop : -0.35 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 129 HIS 0.005 0.001 HIS B 82 PHE 0.035 0.001 PHE A 234 TYR 0.013 0.001 TYR E 59 ARG 0.006 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.02976 ( 391) hydrogen bonds : angle 3.79329 ( 1137) SS BOND : bond 0.00069 ( 3) SS BOND : angle 0.45325 ( 6) covalent geometry : bond 0.00254 ( 8505) covalent geometry : angle 0.51339 (11570) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4557.14 seconds wall clock time: 79 minutes 32.27 seconds (4772.27 seconds total)