Starting phenix.real_space_refine on Wed Mar 12 16:47:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7um6_26598/03_2025/7um6_26598.cif Found real_map, /net/cci-nas-00/data/ceres_data/7um6_26598/03_2025/7um6_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_2025/7um6_26598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7um6_26598/03_2025/7um6_26598.map" model { file = "/net/cci-nas-00/data/ceres_data/7um6_26598/03_2025/7um6_26598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7um6_26598/03_2025/7um6_26598.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 9} 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: {'GLU:plan': 1, 'ARG: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: {'GLN:plan1': 4, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7} 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, 'GLU:plan': 2, 'ARG:plan': 1, '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: {'GLN:plan1': 1, 'GLU:plan': 7, '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: 5.14, per 1000 atoms: 0.63 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: 2.05 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.96 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: 2.42 Time building geometry restraints manager: 2.41 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.000 Find NCS groups from input model: 0.090 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:13.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.420 ------------------------------------------------------------------------------- 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 8355 Z= 0.239 Angle : 0.584 9.010 11387 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), 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 TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS C 142 PHE 0.020 0.001 PHE A 218 TYR 0.017 0.001 TYR A 338 ARG 0.002 0.000 ARG C 256 *********************** 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 : 0.919 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: 0.8637 time to fit residues: 196.9440 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 : 0.826 ------------------------------------------------------------------------------- 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 90 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 0.0980 chunk 83 optimal weight: 7.9990 chunk 32 optimal weight: 0.1980 chunk 50 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.108757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.093916 restraints weight = 11830.681| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.74 r_work: 0.3086 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8355 Z= 0.196 Angle : 0.567 7.059 11387 Z= 0.302 Chirality : 0.043 0.149 1331 Planarity : 0.004 0.030 1432 Dihedral : 4.669 43.503 1192 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.63 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.26), residues: 1074 helix: 1.53 (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 TRP 0.017 0.002 TRP A 117 HIS 0.002 0.001 HIS C 142 PHE 0.019 0.001 PHE A 55 TYR 0.015 0.001 TYR E 178 ARG 0.002 0.000 ARG C 251 *********************** 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 208 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 195 time to evaluate : 0.927 Fit side-chains REVERT: A 330 ASN cc_start: 0.7854 (t0) cc_final: 0.7371 (t0) REVERT: E 87 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7884 (mtt-85) outliers start: 13 outliers final: 9 residues processed: 200 average time/residue: 0.8457 time to fit residues: 183.4349 Evaluate side-chains 195 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 185 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 82 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 100 optimal weight: 3.9990 chunk 39 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.109702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.094621 restraints weight = 11908.167| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.77 r_work: 0.3104 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8355 Z= 0.180 Angle : 0.532 7.076 11387 Z= 0.279 Chirality : 0.042 0.143 1331 Planarity : 0.003 0.027 1432 Dihedral : 4.582 45.111 1190 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.66 % Allowed : 13.41 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.26), residues: 1074 helix: 2.03 (0.29), residues: 347 sheet: 1.02 (0.31), residues: 273 loop : -1.41 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.002 0.001 HIS C 142 PHE 0.024 0.001 PHE A 55 TYR 0.013 0.001 TYR E 178 ARG 0.002 0.000 ARG C 251 *********************** 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 211 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 1.240 Fit side-chains REVERT: A 330 ASN cc_start: 0.7853 (t0) cc_final: 0.7434 (t0) REVERT: B 182 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7890 (mmtt) REVERT: E 87 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.8020 (mtt-85) outliers start: 22 outliers final: 17 residues processed: 195 average time/residue: 0.8796 time to fit residues: 185.9615 Evaluate side-chains 205 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 296 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 315 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 22 ARG Chi-restraints excluded: chain C residue 189 SER 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 42 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 22 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 2 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.094261 restraints weight = 11823.034| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.76 r_work: 0.3096 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8355 Z= 0.195 Angle : 0.537 8.133 11387 Z= 0.281 Chirality : 0.042 0.138 1331 Planarity : 0.003 0.028 1432 Dihedral : 4.666 51.275 1190 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.26 % Allowed : 14.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.26), residues: 1074 helix: 2.22 (0.29), residues: 345 sheet: 0.99 (0.31), residues: 273 loop : -1.42 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.002 0.001 HIS E 35 PHE 0.022 0.001 PHE A 55 TYR 0.013 0.001 TYR E 178 ARG 0.002 0.000 ARG C 251 *********************** 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 212 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.815 Fit side-chains REVERT: A 168 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8412 (tt) REVERT: B 182 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.7997 (mmtt) REVERT: E 87 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7996 (mtt180) outliers start: 27 outliers final: 19 residues processed: 193 average time/residue: 0.8795 time to fit residues: 183.4576 Evaluate side-chains 204 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 296 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 182 LYS 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 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 12 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.109215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.094224 restraints weight = 11678.759| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.73 r_work: 0.3093 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8355 Z= 0.220 Angle : 0.555 8.595 11387 Z= 0.290 Chirality : 0.043 0.141 1331 Planarity : 0.003 0.029 1432 Dihedral : 4.820 58.702 1190 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.14 % Allowed : 14.49 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1074 helix: 2.20 (0.29), residues: 349 sheet: 0.93 (0.31), residues: 279 loop : -1.39 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.002 0.001 HIS C 225 PHE 0.023 0.001 PHE A 55 TYR 0.014 0.001 TYR E 178 ARG 0.002 0.000 ARG C 251 *********************** 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 211 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.892 Fit side-chains REVERT: A 168 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8387 (tt) REVERT: B 182 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8184 (mmtt) REVERT: E 87 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7946 (mtt-85) outliers start: 26 outliers final: 22 residues processed: 194 average time/residue: 0.8754 time to fit residues: 183.4141 Evaluate side-chains 208 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER 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 296 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 315 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 182 LYS 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 102 optimal weight: 0.0470 chunk 42 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.110130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095158 restraints weight = 11821.402| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.74 r_work: 0.3110 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8355 Z= 0.179 Angle : 0.524 6.876 11387 Z= 0.276 Chirality : 0.042 0.140 1331 Planarity : 0.003 0.036 1432 Dihedral : 4.625 52.394 1190 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.14 % Allowed : 14.98 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1074 helix: 2.44 (0.29), residues: 345 sheet: 0.96 (0.31), residues: 279 loop : -1.46 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.002 0.001 HIS E 35 PHE 0.023 0.001 PHE A 55 TYR 0.013 0.001 TYR E 178 ARG 0.002 0.000 ARG E 98 *********************** 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: 26 poor density : 180 time to evaluate : 0.807 Fit side-chains REVERT: A 168 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8413 (tt) REVERT: B 182 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8142 (mmtt) REVERT: E 87 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.8028 (mtt180) REVERT: E 226 THR cc_start: 0.8915 (p) cc_final: 0.8685 (m) outliers start: 26 outliers final: 21 residues processed: 190 average time/residue: 0.9183 time to fit residues: 188.4201 Evaluate side-chains 204 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 296 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 315 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 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 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 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 23 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 0.0030 chunk 80 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.109390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.094393 restraints weight = 11764.015| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.74 r_work: 0.3098 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8355 Z= 0.211 Angle : 0.557 8.510 11387 Z= 0.291 Chirality : 0.043 0.143 1331 Planarity : 0.003 0.038 1432 Dihedral : 4.602 38.416 1190 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.62 % Allowed : 15.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.26), residues: 1074 helix: 2.40 (0.29), residues: 343 sheet: 0.95 (0.31), residues: 279 loop : -1.48 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.002 0.001 HIS C 225 PHE 0.024 0.001 PHE A 55 TYR 0.013 0.001 TYR E 178 ARG 0.002 0.000 ARG E 98 *********************** 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 209 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.930 Fit side-chains REVERT: A 168 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8386 (tt) REVERT: B 182 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8179 (mmtt) REVERT: E 87 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7982 (mtt180) REVERT: E 226 THR cc_start: 0.8924 (p) cc_final: 0.8697 (m) outliers start: 30 outliers final: 24 residues processed: 191 average time/residue: 0.8924 time to fit residues: 184.0667 Evaluate side-chains 205 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER 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 219 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 46 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 112 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 68 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 34 optimal weight: 0.0370 chunk 18 optimal weight: 10.0000 chunk 4 optimal weight: 0.6980 overall best weight: 0.8860 ------------------------------------------------------------------------------- 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 E 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.107937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.092928 restraints weight = 12058.738| |-----------------------------------------------------------------------------| 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: 3.86 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8355 Z= 0.239 Angle : 0.578 8.286 11387 Z= 0.302 Chirality : 0.043 0.149 1331 Planarity : 0.004 0.040 1432 Dihedral : 4.579 30.280 1189 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.86 % Allowed : 15.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.26), residues: 1074 helix: 2.22 (0.29), residues: 347 sheet: 0.91 (0.31), residues: 279 loop : -1.46 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.003 0.001 HIS C 225 PHE 0.029 0.002 PHE A 218 TYR 0.013 0.001 TYR E 178 ARG 0.003 0.000 ARG E 98 *********************** 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 213 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 1.773 Fit side-chains REVERT: A 168 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8396 (tt) REVERT: B 182 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8180 (mmtt) REVERT: C 22 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7841 (mtm180) REVERT: E 87 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.8014 (mtt-85) REVERT: E 226 THR cc_start: 0.8936 (p) cc_final: 0.8698 (m) outliers start: 32 outliers final: 26 residues processed: 193 average time/residue: 1.0287 time to fit residues: 214.3759 Evaluate side-chains 210 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER 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 219 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 112 VAL 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 12 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.109550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.094525 restraints weight = 11892.435| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.75 r_work: 0.3099 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8355 Z= 0.204 Angle : 0.552 8.490 11387 Z= 0.289 Chirality : 0.043 0.148 1331 Planarity : 0.003 0.041 1432 Dihedral : 4.476 30.311 1189 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.74 % Allowed : 15.34 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1074 helix: 2.37 (0.29), residues: 345 sheet: 0.91 (0.30), residues: 279 loop : -1.49 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.002 0.001 HIS C 225 PHE 0.029 0.002 PHE A 218 TYR 0.013 0.001 TYR E 178 ARG 0.002 0.000 ARG E 98 *********************** 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 214 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.914 Fit side-chains REVERT: A 168 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8381 (tt) REVERT: A 336 LEU cc_start: 0.8424 (tt) cc_final: 0.8213 (tp) REVERT: B 182 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8190 (mmtt) REVERT: C 22 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7775 (mtm180) REVERT: E 87 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7982 (mtt-85) REVERT: E 226 THR cc_start: 0.8923 (p) cc_final: 0.8690 (m) outliers start: 31 outliers final: 26 residues processed: 194 average time/residue: 1.0431 time to fit residues: 217.9376 Evaluate side-chains 210 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER 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 219 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 112 VAL 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 12 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 102 optimal weight: 0.0370 chunk 72 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 E 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.110268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.095256 restraints weight = 11750.403| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.74 r_work: 0.3110 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8355 Z= 0.183 Angle : 0.542 8.637 11387 Z= 0.284 Chirality : 0.042 0.147 1331 Planarity : 0.003 0.041 1432 Dihedral : 4.387 30.220 1189 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.50 % Allowed : 16.30 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.26), residues: 1074 helix: 2.45 (0.29), residues: 345 sheet: 0.90 (0.31), residues: 279 loop : -1.46 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.002 0.001 HIS E 35 PHE 0.029 0.001 PHE A 218 TYR 0.013 0.001 TYR E 178 ARG 0.002 0.000 ARG E 98 ********************** 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 207 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.929 Fit side-chains REVERT: A 168 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8416 (tt) REVERT: A 336 LEU cc_start: 0.8377 (tt) cc_final: 0.8163 (tp) REVERT: B 182 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8129 (mmtt) REVERT: C 22 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7822 (mtm180) REVERT: E 87 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.8028 (mtt180) REVERT: E 226 THR cc_start: 0.8921 (p) cc_final: 0.8686 (m) outliers start: 29 outliers final: 23 residues processed: 186 average time/residue: 0.9544 time to fit residues: 191.1467 Evaluate side-chains 204 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER 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 219 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 22 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 98 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 33 optimal weight: 0.4980 chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.109610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.094579 restraints weight = 11850.015| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.75 r_work: 0.3099 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8355 Z= 0.209 Angle : 0.558 8.687 11387 Z= 0.292 Chirality : 0.043 0.182 1331 Planarity : 0.003 0.041 1432 Dihedral : 4.471 30.478 1189 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.74 % Allowed : 15.94 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1074 helix: 2.36 (0.29), residues: 345 sheet: 0.90 (0.31), residues: 279 loop : -1.48 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.002 0.001 HIS C 225 PHE 0.029 0.002 PHE A 218 TYR 0.013 0.001 TYR E 95 ARG 0.002 0.000 ARG C 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6859.86 seconds wall clock time: 119 minutes 39.33 seconds (7179.33 seconds total)