Starting phenix.real_space_refine on Wed Sep 17 11:09:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ary_43798/09_2025/9ary_43798.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ary_43798/09_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_43798/09_2025/9ary_43798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ary_43798/09_2025/9ary_43798.map" model { file = "/net/cci-nas-00/data/ceres_data/9ary_43798/09_2025/9ary_43798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ary_43798/09_2025/9ary_43798.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 3, 'TYR:plan': 2, 'PHE:plan': 2, 'ARG:plan': 2, 'ASP:plan': 5} 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, 'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 4} 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: {'ARG:plan': 4, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN: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: {'ARG:plan': 1, 'GLU: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: {'GLU:plan': 5, 'GLN:plan1': 1, '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: 2.29, per 1000 atoms: 0.27 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: 0.66 Conformation dependent library (CDL) restraints added in 501.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.34 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: 1.22 Time building geometry restraints manager: 0.94 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: 3.020 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.590 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.190 ------------------------------------------------------------------------------- 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 : 3.74 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (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 ARG 0.007 0.001 ARG B 135 TYR 0.014 0.002 TYR B 163 PHE 0.015 0.001 PHE A 244 TRP 0.031 0.002 TRP B 129 HIS 0.005 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 8505) covalent geometry : angle 0.77207 (11570) SS BOND : bond 0.00154 ( 3) SS BOND : angle 0.74988 ( 6) hydrogen bonds : bond 0.17835 ( 391) hydrogen bonds : angle 6.52410 ( 1137) *********************** 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 : 0.290 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: 0.1087 time to fit residues: 20.2540 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 : 0.311 ------------------------------------------------------------------------------- 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 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 B 82 HIS C 156 GLN C 239 ASN E 35 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.176452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.147533 restraints weight = 10160.804| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.36 r_work: 0.3526 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8508 Z= 0.158 Angle : 0.562 8.546 11576 Z= 0.294 Chirality : 0.042 0.139 1347 Planarity : 0.004 0.042 1471 Dihedral : 4.438 31.698 1191 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.33 % Allowed : 14.44 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.25), residues: 1087 helix: 1.28 (0.27), residues: 364 sheet: -0.13 (0.32), residues: 261 loop : -0.70 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 208 TYR 0.018 0.002 TYR E 59 PHE 0.011 0.001 PHE E 29 TRP 0.016 0.002 TRP C 169 HIS 0.004 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8505) covalent geometry : angle 0.56231 (11570) SS BOND : bond 0.00068 ( 3) SS BOND : angle 0.67202 ( 6) hydrogen bonds : bond 0.03836 ( 391) hydrogen bonds : angle 4.30495 ( 1137) *********************** 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 153 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.8088 (mmt) cc_final: 0.7869 (mmm) REVERT: B 14 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7661 (tt0) REVERT: C 135 VAL cc_start: 0.8400 (t) cc_final: 0.8194 (p) REVERT: E 87 ARG cc_start: 0.7634 (ptp-170) cc_final: 0.7388 (mtt90) REVERT: E 211 ASP cc_start: 0.8166 (t0) cc_final: 0.7657 (t0) outliers start: 20 outliers final: 11 residues processed: 150 average time/residue: 0.1027 time to fit residues: 20.6156 Evaluate side-chains 133 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 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 C residue 47 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain E residue 231 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 5 optimal weight: 10.0000 chunk 65 optimal weight: 0.2980 chunk 85 optimal weight: 0.0470 chunk 24 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- 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 343 ASN C 155 ASN C 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.176787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.148530 restraints weight = 10038.166| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.21 r_work: 0.3552 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8508 Z= 0.113 Angle : 0.508 8.012 11576 Z= 0.262 Chirality : 0.041 0.132 1347 Planarity : 0.003 0.034 1471 Dihedral : 4.141 33.249 1189 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.03 % Allowed : 15.60 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.26), residues: 1087 helix: 1.79 (0.28), residues: 364 sheet: -0.07 (0.32), residues: 267 loop : -0.67 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 32 TYR 0.015 0.001 TYR B 115 PHE 0.011 0.001 PHE E 29 TRP 0.015 0.001 TRP C 169 HIS 0.005 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8505) covalent geometry : angle 0.50779 (11570) SS BOND : bond 0.00106 ( 3) SS BOND : angle 0.49773 ( 6) hydrogen bonds : bond 0.03355 ( 391) hydrogen bonds : angle 4.01131 ( 1137) *********************** 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 163 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.329 Fit side-chains REVERT: A 164 MET cc_start: 0.8155 (mmt) cc_final: 0.7934 (mmm) REVERT: B 14 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7812 (tt0) REVERT: B 188 ARG cc_start: 0.7378 (ttt180) cc_final: 0.6985 (mtm110) REVERT: B 233 ASP cc_start: 0.8248 (t0) cc_final: 0.8023 (t0) REVERT: C 155 ASN cc_start: 0.8278 (t0) cc_final: 0.8020 (t0) REVERT: E 211 ASP cc_start: 0.8184 (t0) cc_final: 0.7748 (t0) outliers start: 26 outliers final: 17 residues processed: 156 average time/residue: 0.1089 time to fit residues: 22.6624 Evaluate side-chains 142 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 185 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 28 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 65 optimal weight: 0.0970 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.170703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.142108 restraints weight = 10307.611| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.30 r_work: 0.3470 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8508 Z= 0.171 Angle : 0.572 10.017 11576 Z= 0.295 Chirality : 0.042 0.140 1347 Planarity : 0.004 0.035 1471 Dihedral : 4.320 32.301 1189 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.84 % Allowed : 16.30 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.26), residues: 1087 helix: 1.82 (0.28), residues: 364 sheet: -0.17 (0.32), residues: 263 loop : -0.62 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 185 TYR 0.021 0.002 TYR E 59 PHE 0.013 0.001 PHE C 241 TRP 0.014 0.002 TRP B 129 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 8505) covalent geometry : angle 0.57214 (11570) SS BOND : bond 0.00044 ( 3) SS BOND : angle 0.66211 ( 6) hydrogen bonds : bond 0.03575 ( 391) hydrogen bonds : angle 4.07433 ( 1137) *********************** 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 164 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.318 Fit side-chains REVERT: A 141 TRP cc_start: 0.6024 (OUTLIER) cc_final: 0.5496 (t60) REVERT: A 164 MET cc_start: 0.8186 (mmt) cc_final: 0.7950 (mmm) REVERT: B 14 GLU cc_start: 0.8498 (tm-30) cc_final: 0.7833 (tt0) REVERT: B 82 HIS cc_start: 0.8189 (t70) cc_final: 0.7545 (t70) REVERT: B 188 ARG cc_start: 0.7377 (ttt180) cc_final: 0.6835 (mtm110) REVERT: B 233 ASP cc_start: 0.8313 (t0) cc_final: 0.8049 (t0) REVERT: C 155 ASN cc_start: 0.8271 (t0) cc_final: 0.8014 (t0) REVERT: D 47 GLU cc_start: 0.8245 (tt0) cc_final: 0.7939 (tt0) REVERT: E 79 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6779 (pt) REVERT: E 211 ASP cc_start: 0.8053 (t0) cc_final: 0.7564 (t0) outliers start: 33 outliers final: 24 residues processed: 152 average time/residue: 0.0977 time to fit residues: 20.3945 Evaluate side-chains 142 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 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 101 MET 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 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 162 LEU 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 38 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.0170 chunk 12 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.169799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.139099 restraints weight = 10434.786| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.69 r_work: 0.3444 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3020 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= 0.113 Angle : 0.511 6.858 11576 Z= 0.264 Chirality : 0.040 0.130 1347 Planarity : 0.003 0.032 1471 Dihedral : 4.161 36.985 1189 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.38 % Allowed : 18.74 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.26), residues: 1087 helix: 1.85 (0.28), residues: 370 sheet: -0.07 (0.33), residues: 261 loop : -0.52 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 388 TYR 0.013 0.001 TYR E 178 PHE 0.021 0.001 PHE A 234 TRP 0.014 0.001 TRP C 169 HIS 0.004 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8505) covalent geometry : angle 0.51136 (11570) SS BOND : bond 0.00046 ( 3) SS BOND : angle 0.45878 ( 6) hydrogen bonds : bond 0.03105 ( 391) hydrogen bonds : angle 3.93374 ( 1137) *********************** 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 155 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.337 Fit side-chains REVERT: A 141 TRP cc_start: 0.5835 (OUTLIER) cc_final: 0.5324 (t60) REVERT: A 164 MET cc_start: 0.7977 (mmt) cc_final: 0.7768 (mmm) REVERT: B 14 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7831 (tt0) REVERT: B 82 HIS cc_start: 0.8042 (t70) cc_final: 0.7500 (t70) REVERT: B 188 ARG cc_start: 0.7334 (ttt180) cc_final: 0.7065 (mtp85) REVERT: B 233 ASP cc_start: 0.8068 (t0) cc_final: 0.7822 (t0) REVERT: C 75 GLN cc_start: 0.7681 (tm-30) cc_final: 0.7450 (tm-30) REVERT: C 155 ASN cc_start: 0.8206 (t0) cc_final: 0.7967 (t0) REVERT: D 47 GLU cc_start: 0.8197 (tt0) cc_final: 0.7852 (tt0) REVERT: E 211 ASP cc_start: 0.8063 (t0) cc_final: 0.7601 (t0) outliers start: 29 outliers final: 20 residues processed: 147 average time/residue: 0.0915 time to fit residues: 18.5179 Evaluate side-chains 143 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 141 TRP 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 A residue 334 VAL 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 242 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 70 LEU 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 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 192 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 42 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.167976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.137938 restraints weight = 10330.259| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.56 r_work: 0.3423 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3305 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= 0.139 Angle : 0.529 8.114 11576 Z= 0.274 Chirality : 0.041 0.136 1347 Planarity : 0.003 0.032 1471 Dihedral : 4.167 33.252 1189 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.84 % Allowed : 18.51 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.26), residues: 1087 helix: 1.89 (0.28), residues: 370 sheet: -0.15 (0.33), residues: 263 loop : -0.44 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 185 TYR 0.012 0.001 TYR E 178 PHE 0.027 0.001 PHE A 234 TRP 0.015 0.002 TRP B 129 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8505) covalent geometry : angle 0.52937 (11570) SS BOND : bond 0.00066 ( 3) SS BOND : angle 0.59419 ( 6) hydrogen bonds : bond 0.03279 ( 391) hydrogen bonds : angle 3.96080 ( 1137) *********************** 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 157 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.270 Fit side-chains REVERT: A 141 TRP cc_start: 0.5932 (OUTLIER) cc_final: 0.5359 (t60) REVERT: A 164 MET cc_start: 0.7978 (mmt) cc_final: 0.7757 (mmm) REVERT: B 14 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7818 (tt0) REVERT: B 75 GLN cc_start: 0.7465 (tt0) cc_final: 0.7242 (tt0) REVERT: B 82 HIS cc_start: 0.8073 (t70) cc_final: 0.7692 (t70) REVERT: B 188 ARG cc_start: 0.7366 (ttt180) cc_final: 0.7096 (mtp85) REVERT: B 233 ASP cc_start: 0.8089 (t0) cc_final: 0.7832 (t0) REVERT: C 155 ASN cc_start: 0.8219 (t0) cc_final: 0.7992 (t0) REVERT: D 47 GLU cc_start: 0.8214 (tt0) cc_final: 0.7848 (tt0) REVERT: E 79 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6553 (pt) REVERT: E 211 ASP cc_start: 0.8007 (t0) cc_final: 0.7519 (t0) outliers start: 33 outliers final: 24 residues processed: 148 average time/residue: 0.0909 time to fit residues: 18.8421 Evaluate side-chains 146 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 141 TRP 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 A residue 334 VAL 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 18 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 146 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 66 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 74 optimal weight: 0.0980 chunk 104 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.166768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.136389 restraints weight = 10574.229| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.89 r_work: 0.3405 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8508 Z= 0.145 Angle : 0.529 8.251 11576 Z= 0.275 Chirality : 0.041 0.135 1347 Planarity : 0.003 0.032 1471 Dihedral : 4.197 33.620 1189 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.49 % Allowed : 19.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.26), residues: 1087 helix: 1.98 (0.28), residues: 368 sheet: -0.08 (0.33), residues: 269 loop : -0.37 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 388 TYR 0.018 0.001 TYR C 145 PHE 0.031 0.001 PHE A 234 TRP 0.017 0.002 TRP B 129 HIS 0.003 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8505) covalent geometry : angle 0.52855 (11570) SS BOND : bond 0.00224 ( 3) SS BOND : angle 0.59478 ( 6) hydrogen bonds : bond 0.03271 ( 391) hydrogen bonds : angle 3.94261 ( 1137) *********************** 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 162 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.441 Fit side-chains REVERT: A 141 TRP cc_start: 0.5957 (OUTLIER) cc_final: 0.5405 (t60) REVERT: A 164 MET cc_start: 0.7989 (mmt) cc_final: 0.7767 (mmm) REVERT: B 14 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7841 (tt0) REVERT: B 28 GLU cc_start: 0.7029 (tp30) cc_final: 0.6296 (mt-10) REVERT: B 82 HIS cc_start: 0.8157 (t70) cc_final: 0.7662 (t70) REVERT: B 188 ARG cc_start: 0.7019 (ttt180) cc_final: 0.6737 (mtp85) REVERT: B 233 ASP cc_start: 0.8136 (t0) cc_final: 0.7863 (t0) REVERT: C 155 ASN cc_start: 0.8236 (t0) cc_final: 0.8006 (t0) REVERT: E 79 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6496 (pt) REVERT: E 211 ASP cc_start: 0.8001 (t0) cc_final: 0.7488 (t0) outliers start: 30 outliers final: 24 residues processed: 154 average time/residue: 0.0947 time to fit residues: 19.9501 Evaluate side-chains 155 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 141 TRP 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 A residue 334 VAL 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 70 LEU Chi-restraints excluded: chain C residue 130 GLU 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 Chi-restraints excluded: chain E residue 194 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 73 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 41 optimal weight: 0.0010 chunk 106 optimal weight: 2.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.168283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.137857 restraints weight = 10465.790| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.89 r_work: 0.3426 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8508 Z= 0.119 Angle : 0.511 9.128 11576 Z= 0.264 Chirality : 0.041 0.147 1347 Planarity : 0.003 0.030 1471 Dihedral : 4.077 32.938 1189 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.27), residues: 1087 helix: 2.03 (0.28), residues: 370 sheet: -0.12 (0.34), residues: 259 loop : -0.37 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 388 TYR 0.015 0.001 TYR C 145 PHE 0.012 0.001 PHE E 29 TRP 0.019 0.001 TRP B 129 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8505) covalent geometry : angle 0.51147 (11570) SS BOND : bond 0.00051 ( 3) SS BOND : angle 0.54010 ( 6) hydrogen bonds : bond 0.03106 ( 391) hydrogen bonds : angle 3.85349 ( 1137) *********************** 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 : 0.280 Fit side-chains REVERT: A 141 TRP cc_start: 0.5911 (OUTLIER) cc_final: 0.5293 (t60) REVERT: A 164 MET cc_start: 0.7977 (mmt) cc_final: 0.7763 (mmm) REVERT: B 14 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7880 (tt0) REVERT: B 28 GLU cc_start: 0.7031 (tp30) cc_final: 0.6305 (mt-10) REVERT: B 82 HIS cc_start: 0.8101 (t70) cc_final: 0.7651 (t70) REVERT: B 188 ARG cc_start: 0.6987 (ttt180) cc_final: 0.6693 (mtp85) REVERT: B 233 ASP cc_start: 0.8086 (t0) cc_final: 0.7827 (t0) REVERT: C 42 ARG cc_start: 0.7577 (tmm-80) cc_final: 0.7280 (ttt180) REVERT: C 155 ASN cc_start: 0.8228 (t0) cc_final: 0.7990 (t0) REVERT: E 79 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6466 (pt) REVERT: E 211 ASP cc_start: 0.7951 (t0) cc_final: 0.7494 (t0) outliers start: 28 outliers final: 24 residues processed: 153 average time/residue: 0.0907 time to fit residues: 19.5155 Evaluate side-chains 156 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 141 TRP 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 A residue 334 VAL 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 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 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 194 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 32 optimal weight: 0.0770 chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 0.0570 chunk 105 optimal weight: 0.6980 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 E 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.169855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.139451 restraints weight = 10472.684| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.91 r_work: 0.3443 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 : 0.002 0.028 8508 Z= 0.104 Angle : 0.497 9.796 11576 Z= 0.257 Chirality : 0.040 0.137 1347 Planarity : 0.003 0.029 1471 Dihedral : 3.995 35.064 1189 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.14 % Allowed : 19.44 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.27), residues: 1087 helix: 2.17 (0.28), residues: 370 sheet: -0.02 (0.33), residues: 261 loop : -0.32 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 388 TYR 0.014 0.001 TYR C 145 PHE 0.021 0.001 PHE A 234 TRP 0.020 0.001 TRP B 129 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8505) covalent geometry : angle 0.49683 (11570) SS BOND : bond 0.00040 ( 3) SS BOND : angle 0.41615 ( 6) hydrogen bonds : bond 0.02951 ( 391) hydrogen bonds : angle 3.77428 ( 1137) *********************** 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 155 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.337 Fit side-chains REVERT: A 114 MET cc_start: 0.7666 (ptm) cc_final: 0.6475 (tpt) REVERT: A 141 TRP cc_start: 0.5726 (OUTLIER) cc_final: 0.5182 (t60) REVERT: B 14 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7944 (tt0) REVERT: B 28 GLU cc_start: 0.7012 (tp30) cc_final: 0.6302 (mt-10) REVERT: B 75 GLN cc_start: 0.7542 (tt0) cc_final: 0.7312 (tt0) REVERT: B 82 HIS cc_start: 0.8090 (t70) cc_final: 0.7652 (t70) REVERT: B 188 ARG cc_start: 0.6989 (ttt180) cc_final: 0.6438 (mtp85) REVERT: B 233 ASP cc_start: 0.8055 (t0) cc_final: 0.7803 (t0) REVERT: C 42 ARG cc_start: 0.7566 (tmm-80) cc_final: 0.7315 (ttt180) REVERT: C 118 ASP cc_start: 0.8390 (p0) cc_final: 0.8001 (p0) REVERT: C 155 ASN cc_start: 0.8144 (t0) cc_final: 0.7907 (t0) REVERT: E 79 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6482 (pt) REVERT: E 211 ASP cc_start: 0.7962 (t0) cc_final: 0.7514 (t0) outliers start: 27 outliers final: 22 residues processed: 147 average time/residue: 0.0985 time to fit residues: 19.9554 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 : 0.321 ------------------------------------------------------------------------------- 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 135 ILE Chi-restraints excluded: chain A residue 141 TRP 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 A residue 334 VAL 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 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 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 150 SER Chi-restraints excluded: chain E residue 194 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 21 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 62 optimal weight: 0.0770 chunk 54 optimal weight: 0.0980 chunk 76 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.170365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.140167 restraints weight = 10379.484| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.63 r_work: 0.3464 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8508 Z= 0.104 Angle : 0.503 10.854 11576 Z= 0.260 Chirality : 0.040 0.132 1347 Planarity : 0.003 0.029 1471 Dihedral : 3.963 35.572 1189 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.68 % Allowed : 20.14 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.27), residues: 1087 helix: 2.24 (0.28), residues: 370 sheet: 0.05 (0.33), residues: 260 loop : -0.29 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 388 TYR 0.013 0.001 TYR C 145 PHE 0.013 0.001 PHE A 186 TRP 0.023 0.001 TRP B 129 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8505) covalent geometry : angle 0.50326 (11570) SS BOND : bond 0.00036 ( 3) SS BOND : angle 0.41410 ( 6) hydrogen bonds : bond 0.02922 ( 391) hydrogen bonds : angle 3.72660 ( 1137) ********************** 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 149 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.369 Fit side-chains REVERT: A 114 MET cc_start: 0.7762 (ptm) cc_final: 0.6522 (tpt) REVERT: A 141 TRP cc_start: 0.5742 (OUTLIER) cc_final: 0.5218 (t60) REVERT: B 14 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8043 (tt0) REVERT: B 28 GLU cc_start: 0.7020 (tp30) cc_final: 0.6298 (mt-10) REVERT: B 82 HIS cc_start: 0.8225 (t70) cc_final: 0.7784 (t70) REVERT: B 188 ARG cc_start: 0.7069 (ttt180) cc_final: 0.6504 (mtp85) REVERT: B 233 ASP cc_start: 0.8222 (t0) cc_final: 0.7973 (t0) REVERT: C 118 ASP cc_start: 0.8586 (p0) cc_final: 0.8150 (p0) REVERT: C 155 ASN cc_start: 0.8181 (t0) cc_final: 0.7979 (t0) REVERT: E 79 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6524 (pt) REVERT: E 211 ASP cc_start: 0.8046 (t0) cc_final: 0.7561 (t0) outliers start: 23 outliers final: 21 residues processed: 144 average time/residue: 0.0959 time to fit residues: 19.0679 Evaluate side-chains 145 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 127 VAL 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 171 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 334 VAL 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 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 146 LEU 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 339 TRP Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 194 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 96 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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** C 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.162685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.133348 restraints weight = 10530.741| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.73 r_work: 0.3365 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8508 Z= 0.218 Angle : 0.603 11.014 11576 Z= 0.314 Chirality : 0.044 0.167 1347 Planarity : 0.004 0.034 1471 Dihedral : 4.359 31.681 1189 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.26 % Allowed : 19.67 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.27), residues: 1087 helix: 1.90 (0.28), residues: 368 sheet: -0.17 (0.33), residues: 279 loop : -0.35 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 388 TYR 0.014 0.002 TYR C 145 PHE 0.021 0.002 PHE A 234 TRP 0.023 0.002 TRP B 129 HIS 0.004 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 8505) covalent geometry : angle 0.60255 (11570) SS BOND : bond 0.00072 ( 3) SS BOND : angle 0.84388 ( 6) hydrogen bonds : bond 0.03686 ( 391) hydrogen bonds : angle 4.14589 ( 1137) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2402.49 seconds wall clock time: 41 minutes 50.61 seconds (2510.61 seconds total)