Starting phenix.real_space_refine on Tue Mar 3 18:45:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7um6_26598/03_2026/7um6_26598.cif Found real_map, /net/cci-nas-00/data/ceres_data/7um6_26598/03_2026/7um6_26598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7um6_26598/03_2026/7um6_26598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7um6_26598/03_2026/7um6_26598.map" model { file = "/net/cci-nas-00/data/ceres_data/7um6_26598/03_2026/7um6_26598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7um6_26598/03_2026/7um6_26598.cif" } resolution = 2.79 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= 0.002 sd= 0.027 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 54 5.16 5 C 5236 2.51 5 N 1374 2.21 5 O 1511 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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8175 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1916 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 10, 'TRANS': 247} Chain breaks: 2 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 9, 'GLN:plan1': 4, 'GLU:plan': 6, 'TRP:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 115 Chain: "B" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 2477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2477 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'GLN:plan1': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "D" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 372 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1712 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'H8G': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.24, per 1000 atoms: 0.27 Number of scatterers: 8175 At special positions: 0 Unit cell: (109.2, 115.57, 126.49, 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 54 16.00 O 1511 8.00 N 1374 7.00 C 5236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 114 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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: 0.76 Conformation dependent library (CDL) restraints added in 262.9 milliseconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2048 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 36.5% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 40 through 68 removed outlier: 3.901A pdb=" N LEU A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 55 " --> pdb=" O VAL A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 72 removed outlier: 4.023A pdb=" N HIS A 72 " --> pdb=" O ARG A 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 69 through 72' Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 76 through 92 removed outlier: 3.763A pdb=" N LEU A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 103 removed outlier: 3.590A pdb=" N LEU A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 145 removed outlier: 3.782A pdb=" N CYS A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 122 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS A 124 " --> pdb=" O CYS A 120 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N CYS A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER A 128 " --> pdb=" O CYS A 124 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 179 removed outlier: 3.503A pdb=" N ALA A 163 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TRP A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER A 169 " --> pdb=" O THR A 165 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 197 through 202 removed outlier: 3.820A pdb=" N VAL A 202 " --> pdb=" O PRO A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 209 Processing helix chain 'A' and resid 209 through 230 Processing helix chain 'A' and resid 276 through 297 removed outlier: 3.772A pdb=" N VAL A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 311 removed outlier: 3.837A pdb=" N THR A 304 " --> pdb=" O PRO A 300 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 316 through 329 removed outlier: 3.791A pdb=" N GLY A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 341 removed outlier: 4.429A pdb=" N THR A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE A 341 " --> pdb=" O ILE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 347 Processing helix chain 'B' and resid 3 through 29 removed outlier: 4.055A pdb=" N LYS B 29 " --> pdb=" O ILE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 removed outlier: 4.280A pdb=" N ILE B 94 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N HIS B 95 " --> pdb=" O LYS B 92 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B 98 " --> pdb=" O HIS B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 127 removed outlier: 3.559A pdb=" N SER B 124 " --> pdb=" O MET B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 4.072A pdb=" N ILE B 132 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 150 Processing helix chain 'B' and resid 168 through 181 Processing helix chain 'B' and resid 201 through 220 removed outlier: 3.823A pdb=" N VAL B 205 " --> pdb=" O ASN B 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 25 removed outlier: 3.572A 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: 3.943A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 4.161A 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 9 through 23 removed outlier: 3.921A pdb=" N MET D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.664A pdb=" N CYS D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 removed outlier: 3.642A 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: 3.683A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.849A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 51 through 52 removed outlier: 7.103A pdb=" N LYS B 32 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ILE B 104 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU B 34 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N CYS B 106 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU B 36 " --> pdb=" O CYS B 106 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N ASP B 108 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 103 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N PHE B 139 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE B 105 " --> pdb=" O PHE B 139 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASN B 141 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL B 107 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.743A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.941A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.663A 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: 7.177A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.713A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.775A 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 192 removed outlier: 6.999A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.682A pdb=" N ALA C 231 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.872A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.654A 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 removed outlier: 3.599A pdb=" N SER E 71 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.890A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.890A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.753A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1086 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: 1.49 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1379 1.32 - 1.45: 2292 1.45 - 1.57: 4610 1.57 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 8355 Sorted by residual: bond pdb=" CA SER A 329 " pdb=" CB SER A 329 " ideal model delta sigma weight residual 1.530 1.477 0.054 1.69e-02 3.50e+03 1.00e+01 bond pdb=" C PRO A 335 " pdb=" O PRO A 335 " ideal model delta sigma weight residual 1.235 1.197 0.038 1.30e-02 5.92e+03 8.42e+00 bond pdb=" N ASN A 342 " pdb=" CA ASN A 342 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.23e-02 6.61e+03 7.95e+00 bond pdb=" CAR H8G A 401 " pdb=" CAU H8G A 401 " ideal model delta sigma weight residual 1.418 1.362 0.056 2.00e-02 2.50e+03 7.79e+00 bond pdb=" N GLU B 17 " pdb=" CA GLU B 17 " ideal model delta sigma weight residual 1.459 1.492 -0.034 1.28e-02 6.10e+03 6.92e+00 ... (remaining 8350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 11134 1.80 - 3.60: 215 3.60 - 5.41: 32 5.41 - 7.21: 3 7.21 - 9.01: 3 Bond angle restraints: 11387 Sorted by residual: angle pdb=" N SER A 331 " pdb=" CA SER A 331 " pdb=" C SER A 331 " ideal model delta sigma weight residual 112.92 103.91 9.01 1.23e+00 6.61e-01 5.37e+01 angle pdb=" N ALA A 348 " pdb=" CA ALA A 348 " pdb=" C ALA A 348 " ideal model delta sigma weight residual 112.97 107.04 5.93 1.06e+00 8.90e-01 3.13e+01 angle pdb=" N ASN A 330 " pdb=" CA ASN A 330 " pdb=" C ASN A 330 " ideal model delta sigma weight residual 113.89 105.63 8.26 1.58e+00 4.01e-01 2.73e+01 angle pdb=" N PHE A 332 " pdb=" CA PHE A 332 " pdb=" C PHE A 332 " ideal model delta sigma weight residual 112.68 107.14 5.54 1.33e+00 5.65e-01 1.74e+01 angle pdb=" CA ILE A 337 " pdb=" C ILE A 337 " pdb=" O ILE A 337 " ideal model delta sigma weight residual 121.27 117.02 4.25 1.04e+00 9.25e-01 1.67e+01 ... (remaining 11382 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 4560 16.83 - 33.66: 274 33.66 - 50.49: 48 50.49 - 67.32: 5 67.32 - 84.15: 2 Dihedral angle restraints: 4889 sinusoidal: 1719 harmonic: 3170 Sorted by residual: dihedral pdb=" CA ARG E 179 " pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 164.81 15.19 0 5.00e+00 4.00e-02 9.23e+00 dihedral pdb=" CA CYS E 147 " pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " ideal model delta sinusoidal sigma weight residual 79.00 130.85 -51.85 1 2.00e+01 2.50e-03 9.17e+00 ... (remaining 4886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 979 0.044 - 0.087: 261 0.087 - 0.131: 84 0.131 - 0.174: 6 0.174 - 0.218: 1 Chirality restraints: 1331 Sorted by residual: chirality pdb=" CA LEU A 336 " pdb=" N LEU A 336 " pdb=" C LEU A 336 " pdb=" CB LEU A 336 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA TYR A 328 " pdb=" N TYR A 328 " pdb=" C TYR A 328 " pdb=" CB TYR A 328 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CB ILE B 16 " pdb=" CA ILE B 16 " pdb=" CG1 ILE B 16 " pdb=" CG2 ILE B 16 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 1328 not shown) Planarity restraints: 1432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAJ H8G A 401 " -0.094 2.00e-02 2.50e+03 7.67e-02 1.03e+02 pdb=" CAK H8G A 401 " 0.078 2.00e-02 2.50e+03 pdb=" CAP H8G A 401 " 0.009 2.00e-02 2.50e+03 pdb=" CAV H8G A 401 " -0.029 2.00e-02 2.50e+03 pdb=" NAN H8G A 401 " 0.130 2.00e-02 2.50e+03 pdb=" NAY H8G A 401 " -0.002 2.00e-02 2.50e+03 pdb=" OAD H8G A 401 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAE H8G A 401 " -0.060 2.00e-02 2.50e+03 3.94e-02 1.94e+01 pdb=" CAQ H8G A 401 " -0.019 2.00e-02 2.50e+03 pdb=" CAS H8G A 401 " 0.039 2.00e-02 2.50e+03 pdb=" CAV H8G A 401 " 0.048 2.00e-02 2.50e+03 pdb=" CAW H8G A 401 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 329 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.00e+00 pdb=" C SER A 329 " 0.042 2.00e-02 2.50e+03 pdb=" O SER A 329 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A 330 " -0.015 2.00e-02 2.50e+03 ... (remaining 1429 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 2955 2.87 - 3.38: 6838 3.38 - 3.88: 12377 3.88 - 4.39: 13964 4.39 - 4.90: 25269 Nonbonded interactions: 61403 Sorted by model distance: nonbonded pdb=" NH1 ARG E 190 " pdb=" OD2 ASP E 211 " model vdw 2.359 3.120 nonbonded pdb=" O ALA B 38 " pdb=" OG SER B 41 " model vdw 2.366 3.040 nonbonded pdb=" O ASP C 333 " pdb=" OG SER C 334 " model vdw 2.379 3.040 nonbonded pdb=" OH TYR B 191 " pdb=" OD2 ASP B 212 " model vdw 2.391 3.040 nonbonded pdb=" O THR D 52 " pdb=" OG1 THR D 52 " model vdw 2.399 3.040 ... (remaining 61398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.680 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8357 Z= 0.191 Angle : 0.585 9.010 11391 Z= 0.338 Chirality : 0.043 0.218 1331 Planarity : 0.004 0.077 1432 Dihedral : 11.087 84.149 2835 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.12 % Allowed : 0.60 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 are not related in a simple way. whole: -0.54 (0.25), residues: 1074 helix: -0.07 (0.27), residues: 332 sheet: 0.97 (0.32), residues: 268 loop : -1.34 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 256 TYR 0.017 0.001 TYR A 338 PHE 0.020 0.001 PHE A 218 TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8355) covalent geometry : angle 0.58445 (11387) SS BOND : bond 0.00679 ( 2) SS BOND : angle 1.04433 ( 4) hydrogen bonds : bond 0.30166 ( 384) hydrogen bonds : angle 7.35301 ( 1086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.318 Fit side-chains REVERT: B 201 ASN cc_start: 0.7201 (p0) cc_final: 0.6994 (p0) REVERT: E 218 MET cc_start: 0.8250 (ttp) cc_final: 0.8014 (ttp) outliers start: 1 outliers final: 2 residues processed: 211 average time/residue: 0.4617 time to fit residues: 104.4966 Evaluate side-chains 192 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 339 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 38 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN B 202 ASN C 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.109639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.094770 restraints weight = 11808.147| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.76 r_work: 0.3094 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8357 Z= 0.132 Angle : 0.554 7.136 11391 Z= 0.295 Chirality : 0.042 0.141 1331 Planarity : 0.003 0.029 1432 Dihedral : 4.607 43.362 1192 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.57 % Allowed : 8.82 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 are not related in a simple way. whole: 0.25 (0.26), residues: 1074 helix: 1.48 (0.29), residues: 343 sheet: 0.92 (0.31), residues: 273 loop : -1.38 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 304 TYR 0.014 0.001 TYR E 178 PHE 0.017 0.001 PHE A 55 TRP 0.016 0.001 TRP A 117 HIS 0.002 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8355) covalent geometry : angle 0.55374 (11387) SS BOND : bond 0.00928 ( 2) SS BOND : angle 1.37385 ( 4) hydrogen bonds : bond 0.06850 ( 384) hydrogen bonds : angle 4.45229 ( 1086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 192 time to evaluate : 0.308 Fit side-chains REVERT: A 330 ASN cc_start: 0.7836 (t0) cc_final: 0.7378 (t0) REVERT: E 87 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7877 (mtt-85) outliers start: 13 outliers final: 9 residues processed: 197 average time/residue: 0.4266 time to fit residues: 90.6378 Evaluate side-chains 198 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 188 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 177 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 81 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 97 optimal weight: 0.0170 chunk 7 optimal weight: 0.0010 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 0.0070 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN C 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.110631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.096089 restraints weight = 12246.460| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.76 r_work: 0.3131 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8357 Z= 0.102 Angle : 0.500 6.882 11391 Z= 0.262 Chirality : 0.041 0.142 1331 Planarity : 0.003 0.024 1432 Dihedral : 4.406 45.963 1190 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.29 % Allowed : 12.56 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 are not related in a simple way. whole: 0.60 (0.26), residues: 1074 helix: 2.05 (0.29), residues: 346 sheet: 1.06 (0.31), residues: 271 loop : -1.40 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 190 TYR 0.012 0.001 TYR E 178 PHE 0.026 0.001 PHE A 55 TRP 0.012 0.001 TRP A 117 HIS 0.001 0.000 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 8355) covalent geometry : angle 0.49980 (11387) SS BOND : bond 0.00711 ( 2) SS BOND : angle 1.04461 ( 4) hydrogen bonds : bond 0.04526 ( 384) hydrogen bonds : angle 3.87436 ( 1086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.317 Fit side-chains outliers start: 19 outliers final: 15 residues processed: 189 average time/residue: 0.4676 time to fit residues: 95.1522 Evaluate side-chains 193 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 178 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 118 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN C 75 GLN C 88 ASN C 110 ASN E 77 ASN E 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.108689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.093623 restraints weight = 11921.023| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.77 r_work: 0.3076 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8357 Z= 0.163 Angle : 0.581 7.807 11391 Z= 0.305 Chirality : 0.043 0.143 1331 Planarity : 0.003 0.029 1432 Dihedral : 4.791 50.488 1190 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.90 % Allowed : 14.25 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 are not related in a simple way. whole: 0.56 (0.26), residues: 1074 helix: 2.00 (0.29), residues: 349 sheet: 0.93 (0.31), residues: 279 loop : -1.40 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 251 TYR 0.014 0.002 TYR E 95 PHE 0.022 0.002 PHE A 55 TRP 0.016 0.002 TRP C 82 HIS 0.003 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8355) covalent geometry : angle 0.57946 (11387) SS BOND : bond 0.01123 ( 2) SS BOND : angle 1.97477 ( 4) hydrogen bonds : bond 0.06152 ( 384) hydrogen bonds : angle 4.08657 ( 1086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.302 Fit side-chains REVERT: A 168 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8398 (tt) REVERT: A 336 LEU cc_start: 0.8452 (tp) cc_final: 0.8249 (tt) REVERT: B 182 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8137 (mmtt) REVERT: E 87 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7931 (mtt-85) outliers start: 24 outliers final: 17 residues processed: 195 average time/residue: 0.4402 time to fit residues: 92.5459 Evaluate side-chains 202 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 177 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.107899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.092984 restraints weight = 12126.783| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.80 r_work: 0.3075 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8357 Z= 0.149 Angle : 0.560 8.679 11391 Z= 0.294 Chirality : 0.043 0.144 1331 Planarity : 0.003 0.030 1432 Dihedral : 4.852 57.102 1190 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.14 % Allowed : 14.25 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 are not related in a simple way. whole: 0.57 (0.26), residues: 1074 helix: 2.06 (0.29), residues: 349 sheet: 0.92 (0.30), residues: 279 loop : -1.42 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 98 TYR 0.014 0.001 TYR E 178 PHE 0.022 0.002 PHE A 55 TRP 0.015 0.002 TRP C 82 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8355) covalent geometry : angle 0.55929 (11387) SS BOND : bond 0.01030 ( 2) SS BOND : angle 1.72834 ( 4) hydrogen bonds : bond 0.05648 ( 384) hydrogen bonds : angle 3.96415 ( 1086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.306 Fit side-chains REVERT: A 168 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8396 (tt) REVERT: E 87 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7988 (mtt-85) REVERT: E 226 THR cc_start: 0.8930 (p) cc_final: 0.8696 (m) outliers start: 26 outliers final: 22 residues processed: 195 average time/residue: 0.4312 time to fit residues: 90.5625 Evaluate side-chains 205 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 177 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 103 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 75 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 90 optimal weight: 0.0270 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.110588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.095599 restraints weight = 11736.140| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.76 r_work: 0.3113 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8357 Z= 0.111 Angle : 0.514 6.861 11391 Z= 0.271 Chirality : 0.042 0.140 1331 Planarity : 0.003 0.036 1432 Dihedral : 4.599 53.427 1190 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.90 % Allowed : 14.86 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 are not related in a simple way. whole: 0.69 (0.26), residues: 1074 helix: 2.36 (0.29), residues: 345 sheet: 0.95 (0.30), residues: 279 loop : -1.48 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 98 TYR 0.013 0.001 TYR E 178 PHE 0.022 0.001 PHE A 55 TRP 0.012 0.001 TRP C 82 HIS 0.002 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8355) covalent geometry : angle 0.51395 (11387) SS BOND : bond 0.00794 ( 2) SS BOND : angle 1.20101 ( 4) hydrogen bonds : bond 0.04558 ( 384) hydrogen bonds : angle 3.76634 ( 1086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.327 Fit side-chains REVERT: A 168 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8417 (tt) REVERT: A 333 PHE cc_start: 0.8402 (m-80) cc_final: 0.7949 (m-80) REVERT: B 182 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8148 (mmtt) REVERT: E 226 THR cc_start: 0.8928 (p) cc_final: 0.8691 (m) outliers start: 24 outliers final: 19 residues processed: 192 average time/residue: 0.4511 time to fit residues: 93.3216 Evaluate side-chains 201 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 218 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 28 optimal weight: 0.0970 chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 68 optimal weight: 0.0670 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 0.0570 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.110978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.096027 restraints weight = 12264.360| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.81 r_work: 0.3130 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8357 Z= 0.100 Angle : 0.506 7.387 11391 Z= 0.265 Chirality : 0.042 0.191 1331 Planarity : 0.003 0.040 1432 Dihedral : 4.308 35.254 1190 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.66 % Allowed : 16.06 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 are not related in a simple way. whole: 0.74 (0.26), residues: 1074 helix: 2.44 (0.29), residues: 345 sheet: 0.97 (0.31), residues: 273 loop : -1.45 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 98 TYR 0.013 0.001 TYR E 178 PHE 0.024 0.001 PHE A 55 TRP 0.010 0.001 TRP E 47 HIS 0.002 0.000 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 8355) covalent geometry : angle 0.50545 (11387) SS BOND : bond 0.00669 ( 2) SS BOND : angle 0.97437 ( 4) hydrogen bonds : bond 0.03961 ( 384) hydrogen bonds : angle 3.61405 ( 1086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.268 Fit side-chains REVERT: A 168 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8418 (tt) REVERT: A 333 PHE cc_start: 0.8361 (m-80) cc_final: 0.7934 (m-80) REVERT: B 182 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8065 (mmtt) outliers start: 22 outliers final: 16 residues processed: 186 average time/residue: 0.4250 time to fit residues: 85.1443 Evaluate side-chains 194 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 218 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 0.0030 chunk 16 optimal weight: 0.3980 chunk 87 optimal weight: 0.7980 chunk 97 optimal weight: 0.0170 chunk 71 optimal weight: 0.0970 chunk 32 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.2226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.111959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.097329 restraints weight = 12275.509| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.75 r_work: 0.3154 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8357 Z= 0.092 Angle : 0.489 7.486 11391 Z= 0.256 Chirality : 0.041 0.141 1331 Planarity : 0.003 0.041 1432 Dihedral : 4.050 30.368 1189 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.17 % Allowed : 16.79 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 are not related in a simple way. whole: 0.81 (0.26), residues: 1074 helix: 2.64 (0.29), residues: 336 sheet: 0.96 (0.30), residues: 279 loop : -1.44 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 98 TYR 0.012 0.001 TYR E 178 PHE 0.026 0.001 PHE A 218 TRP 0.009 0.001 TRP E 47 HIS 0.001 0.000 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00197 ( 8355) covalent geometry : angle 0.48929 (11387) SS BOND : bond 0.00553 ( 2) SS BOND : angle 0.78057 ( 4) hydrogen bonds : bond 0.03484 ( 384) hydrogen bonds : angle 3.49774 ( 1086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.320 Fit side-chains REVERT: A 168 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8414 (tt) REVERT: A 333 PHE cc_start: 0.8386 (m-80) cc_final: 0.7986 (m-80) REVERT: B 140 LEU cc_start: 0.8330 (mt) cc_final: 0.7979 (mp) REVERT: B 182 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.7999 (mmtt) REVERT: C 155 ASN cc_start: 0.8348 (t0) cc_final: 0.7983 (t160) outliers start: 18 outliers final: 13 residues processed: 187 average time/residue: 0.4413 time to fit residues: 89.0606 Evaluate side-chains 190 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 218 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 45 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.109984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.094931 restraints weight = 12060.421| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.80 r_work: 0.3113 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8357 Z= 0.120 Angle : 0.538 7.909 11391 Z= 0.281 Chirality : 0.042 0.166 1331 Planarity : 0.003 0.041 1432 Dihedral : 4.241 30.089 1189 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.93 % Allowed : 17.63 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 are not related in a simple way. whole: 0.80 (0.26), residues: 1074 helix: 2.63 (0.29), residues: 337 sheet: 0.88 (0.30), residues: 284 loop : -1.43 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 98 TYR 0.013 0.001 TYR E 178 PHE 0.028 0.001 PHE A 218 TRP 0.012 0.001 TRP C 82 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8355) covalent geometry : angle 0.53771 (11387) SS BOND : bond 0.00846 ( 2) SS BOND : angle 1.43589 ( 4) hydrogen bonds : bond 0.04566 ( 384) hydrogen bonds : angle 3.66609 ( 1086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.334 Fit side-chains REVERT: A 168 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8437 (tt) REVERT: A 333 PHE cc_start: 0.8377 (m-80) cc_final: 0.7931 (m-80) REVERT: B 109 LEU cc_start: 0.8032 (mp) cc_final: 0.7804 (mt) REVERT: B 140 LEU cc_start: 0.8226 (mt) cc_final: 0.7956 (mp) REVERT: B 182 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8113 (mmtt) REVERT: E 226 THR cc_start: 0.8925 (p) cc_final: 0.8681 (m) outliers start: 16 outliers final: 13 residues processed: 188 average time/residue: 0.4392 time to fit residues: 89.1318 Evaluate side-chains 195 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 177 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 3 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 ASN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.107657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.092766 restraints weight = 12058.964| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.80 r_work: 0.3074 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8357 Z= 0.161 Angle : 0.598 8.638 11391 Z= 0.312 Chirality : 0.044 0.215 1331 Planarity : 0.004 0.041 1432 Dihedral : 4.553 30.158 1189 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.93 % Allowed : 17.51 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 are not related in a simple way. whole: 0.60 (0.26), residues: 1074 helix: 2.31 (0.29), residues: 341 sheet: 0.82 (0.30), residues: 284 loop : -1.48 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 98 TYR 0.014 0.002 TYR E 178 PHE 0.029 0.002 PHE A 218 TRP 0.015 0.002 TRP C 82 HIS 0.003 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8355) covalent geometry : angle 0.59750 (11387) SS BOND : bond 0.01048 ( 2) SS BOND : angle 1.93354 ( 4) hydrogen bonds : bond 0.05766 ( 384) hydrogen bonds : angle 3.92431 ( 1086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.244 Fit side-chains REVERT: A 168 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8407 (tt) REVERT: B 140 LEU cc_start: 0.8399 (mt) cc_final: 0.8101 (mp) REVERT: B 182 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8247 (mmtt) REVERT: E 226 THR cc_start: 0.8932 (p) cc_final: 0.8698 (m) outliers start: 16 outliers final: 14 residues processed: 188 average time/residue: 0.4405 time to fit residues: 89.2141 Evaluate side-chains 196 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 177 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.107413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.092504 restraints weight = 12085.006| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.79 r_work: 0.3074 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8357 Z= 0.163 Angle : 0.598 8.724 11391 Z= 0.313 Chirality : 0.044 0.226 1331 Planarity : 0.004 0.042 1432 Dihedral : 4.603 30.083 1189 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.93 % Allowed : 17.51 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 are not related in a simple way. whole: 0.55 (0.26), residues: 1074 helix: 2.26 (0.29), residues: 341 sheet: 0.82 (0.30), residues: 284 loop : -1.52 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 98 TYR 0.014 0.002 TYR E 178 PHE 0.030 0.002 PHE A 218 TRP 0.015 0.002 TRP C 82 HIS 0.003 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 8355) covalent geometry : angle 0.59711 (11387) SS BOND : bond 0.01046 ( 2) SS BOND : angle 1.91560 ( 4) hydrogen bonds : bond 0.05746 ( 384) hydrogen bonds : angle 3.94611 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3329.96 seconds wall clock time: 57 minutes 15.62 seconds (3435.62 seconds total)