Starting phenix.real_space_refine on Wed Sep 17 11:03:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k20_61986/09_2025/9k20_61986.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k20_61986/09_2025/9k20_61986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k20_61986/09_2025/9k20_61986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k20_61986/09_2025/9k20_61986.map" model { file = "/net/cci-nas-00/data/ceres_data/9k20_61986/09_2025/9k20_61986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k20_61986/09_2025/9k20_61986.cif" } resolution = 2.65 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= -0.001 sd= 0.085 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 58 5.16 5 C 5306 2.51 5 N 1416 2.21 5 O 1509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8292 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2233 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 12, 'TRANS': 275} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 5, 'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1608 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5, 'ASN:plan1': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "C" Number of atoms: 2410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2410 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 5, 'TRANS': 325} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 4, 'ASN:plan1': 3, 'ARG:plan': 7, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 91 Chain: "D" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 312 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1698 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.20, per 1000 atoms: 0.27 Number of scatterers: 8292 At special positions: 0 Unit cell: (88.765, 115.827, 135.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 3 15.00 O 1509 8.00 N 1416 7.00 C 5306 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 183 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 487.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 15 sheets defined 37.2% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 31 through 61 Proline residue: A 37 - end of helix Processing helix chain 'A' and resid 68 through 85 Processing helix chain 'A' and resid 85 through 95 removed outlier: 4.293A pdb=" N LEU A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 137 removed outlier: 3.536A pdb=" N ILE A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 143 Processing helix chain 'A' and resid 147 through 166 Processing helix chain 'A' and resid 166 through 172 removed outlier: 3.935A pdb=" N TYR A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 226 removed outlier: 3.715A pdb=" N PHE A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Proline residue: A 210 - end of helix Processing helix chain 'A' and resid 237 through 274 removed outlier: 3.912A pdb=" N VAL A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Proline residue: A 260 - end of helix Processing helix chain 'A' and resid 277 through 308 Proline residue: A 293 - end of helix removed outlier: 4.441A pdb=" N SER A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N CYS A 300 " --> pdb=" O SER A 296 " (cutoff:3.500A) Proline residue: A 303 - end of helix Processing helix chain 'B' and resid 3 through 16 Processing helix chain 'B' and resid 16 through 29 Processing helix chain 'B' and resid 43 through 52 Processing helix chain 'B' and resid 90 through 94 Processing helix chain 'B' and resid 113 through 128 Processing helix chain 'B' and resid 129 through 133 removed outlier: 3.737A pdb=" N ILE B 133 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 152 Processing helix chain 'B' and resid 155 through 159 removed outlier: 3.935A pdb=" N ILE B 158 " --> pdb=" O PRO B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 182 Processing helix chain 'B' and resid 202 through 223 Processing helix chain 'C' and resid 11 through 26 removed outlier: 3.608A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 29 through 44 removed outlier: 4.081A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.535A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 176 Processing sheet with id=AA2, first strand: chain 'B' and resid 68 through 73 removed outlier: 9.713A pdb=" N ALA B 103 " --> pdb=" O ASP B 31 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS B 33 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE B 105 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU B 35 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N CYS B 107 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU B 37 " --> pdb=" O CYS B 107 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N ASP B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE B 104 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N PHE B 140 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE B 106 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASN B 142 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL B 108 " --> pdb=" O ASN B 142 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.592A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.647A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.949A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.711A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.954A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.475A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.797A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.802A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.837A pdb=" N GLY E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.837A pdb=" N GLY E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB6, first strand: chain 'E' and resid 134 through 136 removed outlier: 5.954A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 433 hydrogen bonds defined for protein. 1233 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: 1.38 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2652 1.34 - 1.46: 2102 1.46 - 1.58: 3641 1.58 - 1.70: 5 1.70 - 1.82: 78 Bond restraints: 8478 Sorted by residual: bond pdb=" C6 ATP A 401 " pdb=" N6 ATP A 401 " ideal model delta sigma weight residual 1.337 1.428 -0.091 1.10e-02 8.26e+03 6.86e+01 bond pdb=" C5 ATP A 401 " pdb=" N7 ATP A 401 " ideal model delta sigma weight residual 1.387 1.325 0.062 1.00e-02 1.00e+04 3.85e+01 bond pdb=" C8 ATP A 401 " pdb=" N9 ATP A 401 " ideal model delta sigma weight residual 1.370 1.297 0.073 1.20e-02 6.94e+03 3.74e+01 bond pdb=" C4 ATP A 401 " pdb=" N9 ATP A 401 " ideal model delta sigma weight residual 1.374 1.321 0.053 1.00e-02 1.00e+04 2.76e+01 bond pdb=" C4 ATP A 401 " pdb=" C5 ATP A 401 " ideal model delta sigma weight residual 1.388 1.340 0.048 1.00e-02 1.00e+04 2.29e+01 ... (remaining 8473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.21: 11523 5.21 - 10.43: 28 10.43 - 15.64: 2 15.64 - 20.85: 0 20.85 - 26.06: 2 Bond angle restraints: 11555 Sorted by residual: angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 113.81 26.06 1.00e+00 1.00e+00 6.79e+02 angle pdb=" PA ATP A 401 " pdb=" O3A ATP A 401 " pdb=" PB ATP A 401 " ideal model delta sigma weight residual 136.83 115.31 21.52 1.00e+00 1.00e+00 4.63e+02 angle pdb=" C5' ATP A 401 " pdb=" O5' ATP A 401 " pdb=" PA ATP A 401 " ideal model delta sigma weight residual 121.27 107.59 13.68 1.00e+00 1.00e+00 1.87e+02 angle pdb=" C5 ATP A 401 " pdb=" C4 ATP A 401 " pdb=" N3 ATP A 401 " ideal model delta sigma weight residual 126.80 119.29 7.51 1.00e+00 1.00e+00 5.63e+01 angle pdb=" O3A ATP A 401 " pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " ideal model delta sigma weight residual 101.57 112.80 -11.23 1.54e+00 4.24e-01 5.35e+01 ... (remaining 11550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 4325 17.22 - 34.44: 489 34.44 - 51.65: 127 51.65 - 68.87: 22 68.87 - 86.09: 9 Dihedral angle restraints: 4972 sinusoidal: 1748 harmonic: 3224 Sorted by residual: dihedral pdb=" CB CYS A 25 " pdb=" SG CYS A 25 " pdb=" SG CYS A 278 " pdb=" CB CYS A 278 " ideal model delta sinusoidal sigma weight residual 93.00 142.13 -49.13 1 1.00e+01 1.00e-02 3.32e+01 dihedral pdb=" CA ILE D 28 " pdb=" C ILE D 28 " pdb=" N LYS D 29 " pdb=" CA LYS D 29 " ideal model delta harmonic sigma weight residual 180.00 161.41 18.59 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA TRP C 169 " pdb=" C TRP C 169 " pdb=" N ASP C 170 " pdb=" CA ASP C 170 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 4969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 823 0.030 - 0.061: 344 0.061 - 0.091: 99 0.091 - 0.122: 66 0.122 - 0.152: 14 Chirality restraints: 1346 Sorted by residual: chirality pdb=" CA ASP E 73 " pdb=" N ASP E 73 " pdb=" C ASP E 73 " pdb=" CB ASP E 73 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" C4' ATP A 401 " pdb=" C3' ATP A 401 " pdb=" C5' ATP A 401 " pdb=" O4' ATP A 401 " both_signs ideal model delta sigma weight residual False -2.49 -2.64 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ILE E 177 " pdb=" N ILE E 177 " pdb=" C ILE E 177 " pdb=" CB ILE E 177 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 1343 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 59 " 0.070 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO D 60 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO D 60 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO D 60 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 73 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.42e+00 pdb=" CG ASP E 73 " -0.050 2.00e-02 2.50e+03 pdb=" OD1 ASP E 73 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP E 73 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 36 " 0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO A 37 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 37 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 37 " 0.033 5.00e-02 4.00e+02 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1318 2.76 - 3.29: 7578 3.29 - 3.83: 14366 3.83 - 4.36: 16687 4.36 - 4.90: 29328 Nonbonded interactions: 69277 Sorted by model distance: nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.225 3.040 nonbonded pdb=" O ALA B 178 " pdb=" OG SER B 182 " model vdw 2.284 3.040 nonbonded pdb=" OD1 ASP E 73 " pdb=" OG1 THR E 78 " model vdw 2.296 3.040 nonbonded pdb=" O MET C 325 " pdb=" ND2 ASN C 340 " model vdw 2.305 3.120 nonbonded pdb=" O GLY A 134 " pdb=" ND2 ASN B 219 " model vdw 2.315 3.120 ... (remaining 69272 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: 1.140 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: 0.030 Set scattering table: 0.030 Process input model: 9.770 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 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 0.091 8482 Z= 0.245 Angle : 0.777 26.064 11563 Z= 0.510 Chirality : 0.042 0.152 1346 Planarity : 0.006 0.103 1452 Dihedral : 16.087 86.090 2886 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 26.81 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.25), residues: 1095 helix: 0.89 (0.26), residues: 379 sheet: 0.41 (0.32), residues: 266 loop : -0.84 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 148 TYR 0.017 0.001 TYR E 178 PHE 0.014 0.001 PHE A 113 TRP 0.017 0.001 TRP A 99 HIS 0.003 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 8478) covalent geometry : angle 0.77714 (11555) SS BOND : bond 0.00417 ( 4) SS BOND : angle 0.38594 ( 8) hydrogen bonds : bond 0.17751 ( 419) hydrogen bonds : angle 6.79217 ( 1233) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.343 Fit side-chains REVERT: C 262 MET cc_start: 0.7991 (mmm) cc_final: 0.7672 (tpp) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.5264 time to fit residues: 59.3482 Evaluate side-chains 97 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS C 175 GLN C 183 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.163644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.134211 restraints weight = 11445.278| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.13 r_work: 0.3608 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8482 Z= 0.260 Angle : 0.683 8.524 11563 Z= 0.359 Chirality : 0.045 0.150 1346 Planarity : 0.006 0.059 1452 Dihedral : 7.048 87.738 1234 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 6.04 % Allowed : 21.98 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.25), residues: 1095 helix: 0.91 (0.26), residues: 380 sheet: 0.10 (0.32), residues: 258 loop : -0.96 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 150 TYR 0.024 0.002 TYR E 178 PHE 0.024 0.002 PHE C 151 TRP 0.021 0.002 TRP C 169 HIS 0.008 0.002 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00602 ( 8478) covalent geometry : angle 0.68210 (11555) SS BOND : bond 0.00742 ( 4) SS BOND : angle 1.22132 ( 8) hydrogen bonds : bond 0.05558 ( 419) hydrogen bonds : angle 5.33361 ( 1233) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 102 time to evaluate : 0.323 Fit side-chains REVERT: B 11 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7097 (tm-30) REVERT: B 93 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7270 (mmmt) REVERT: C 262 MET cc_start: 0.8301 (mmm) cc_final: 0.7942 (tpp) outliers start: 50 outliers final: 25 residues processed: 133 average time/residue: 0.4590 time to fit residues: 65.9788 Evaluate side-chains 119 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 105 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 99 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS C 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.166023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.136716 restraints weight = 11268.949| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.13 r_work: 0.3643 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8482 Z= 0.156 Angle : 0.580 7.323 11563 Z= 0.304 Chirality : 0.042 0.146 1346 Planarity : 0.005 0.053 1452 Dihedral : 6.752 85.264 1234 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.35 % Allowed : 23.43 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.25), residues: 1095 helix: 1.23 (0.26), residues: 380 sheet: 0.06 (0.31), residues: 263 loop : -0.93 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 143 TYR 0.017 0.001 TYR E 178 PHE 0.017 0.002 PHE C 151 TRP 0.018 0.002 TRP C 169 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8478) covalent geometry : angle 0.57994 (11555) SS BOND : bond 0.00601 ( 4) SS BOND : angle 0.91697 ( 8) hydrogen bonds : bond 0.04544 ( 419) hydrogen bonds : angle 5.03232 ( 1233) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.331 Fit side-chains REVERT: B 11 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7319 (tt0) REVERT: C 262 MET cc_start: 0.8326 (mmm) cc_final: 0.7953 (tpp) outliers start: 36 outliers final: 20 residues processed: 121 average time/residue: 0.4449 time to fit residues: 58.5504 Evaluate side-chains 118 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 69 optimal weight: 0.0670 chunk 73 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.164781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.135231 restraints weight = 11526.466| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.15 r_work: 0.3625 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8482 Z= 0.190 Angle : 0.620 7.615 11563 Z= 0.321 Chirality : 0.043 0.153 1346 Planarity : 0.005 0.053 1452 Dihedral : 6.865 86.703 1234 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.71 % Allowed : 23.91 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.25), residues: 1095 helix: 1.18 (0.26), residues: 380 sheet: -0.12 (0.31), residues: 265 loop : -0.97 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 148 TYR 0.019 0.002 TYR E 178 PHE 0.019 0.002 PHE C 151 TRP 0.018 0.002 TRP C 169 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 8478) covalent geometry : angle 0.61931 (11555) SS BOND : bond 0.00600 ( 4) SS BOND : angle 1.07077 ( 8) hydrogen bonds : bond 0.04774 ( 419) hydrogen bonds : angle 5.04705 ( 1233) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 103 time to evaluate : 0.349 Fit side-chains REVERT: B 11 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7316 (tt0) REVERT: C 262 MET cc_start: 0.8221 (mmm) cc_final: 0.7907 (tpp) REVERT: E 34 MET cc_start: 0.8272 (mmm) cc_final: 0.8018 (mmp) outliers start: 39 outliers final: 24 residues processed: 129 average time/residue: 0.4733 time to fit residues: 66.0521 Evaluate side-chains 124 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 46 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.164905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134732 restraints weight = 11443.932| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.21 r_work: 0.3607 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8482 Z= 0.190 Angle : 0.616 8.412 11563 Z= 0.320 Chirality : 0.043 0.152 1346 Planarity : 0.005 0.052 1452 Dihedral : 6.873 86.394 1234 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 5.07 % Allowed : 24.40 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.25), residues: 1095 helix: 1.17 (0.26), residues: 380 sheet: -0.22 (0.31), residues: 265 loop : -1.04 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 143 TYR 0.017 0.002 TYR E 178 PHE 0.020 0.002 PHE C 151 TRP 0.018 0.002 TRP C 169 HIS 0.004 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 8478) covalent geometry : angle 0.61509 (11555) SS BOND : bond 0.00578 ( 4) SS BOND : angle 1.08743 ( 8) hydrogen bonds : bond 0.04717 ( 419) hydrogen bonds : angle 5.04760 ( 1233) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 102 time to evaluate : 0.328 Fit side-chains REVERT: A 63 LYS cc_start: 0.4572 (OUTLIER) cc_final: 0.1197 (ptmt) REVERT: B 11 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7249 (tt0) REVERT: B 221 ARG cc_start: 0.7909 (ttp-110) cc_final: 0.7575 (ptp-110) REVERT: C 262 MET cc_start: 0.8237 (mmm) cc_final: 0.7941 (tpp) REVERT: E 34 MET cc_start: 0.8260 (mmm) cc_final: 0.7933 (mmp) outliers start: 42 outliers final: 28 residues processed: 132 average time/residue: 0.4206 time to fit residues: 60.4158 Evaluate side-chains 128 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 0.0270 chunk 57 optimal weight: 0.7980 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS B 202 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.167199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.137694 restraints weight = 11278.305| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.15 r_work: 0.3639 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8482 Z= 0.131 Angle : 0.565 8.832 11563 Z= 0.290 Chirality : 0.041 0.144 1346 Planarity : 0.005 0.072 1452 Dihedral : 6.627 84.252 1234 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.86 % Allowed : 25.36 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.25), residues: 1095 helix: 1.47 (0.27), residues: 380 sheet: -0.09 (0.31), residues: 262 loop : -0.98 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 137 TYR 0.015 0.001 TYR E 178 PHE 0.014 0.001 PHE C 151 TRP 0.019 0.002 TRP C 169 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8478) covalent geometry : angle 0.56531 (11555) SS BOND : bond 0.00688 ( 4) SS BOND : angle 0.74191 ( 8) hydrogen bonds : bond 0.04060 ( 419) hydrogen bonds : angle 4.81677 ( 1233) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.310 Fit side-chains REVERT: B 11 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7275 (tt0) REVERT: B 221 ARG cc_start: 0.7897 (ttp-110) cc_final: 0.7533 (ptp-110) REVERT: C 262 MET cc_start: 0.8216 (mmm) cc_final: 0.7975 (tpp) REVERT: E 34 MET cc_start: 0.8273 (mmm) cc_final: 0.7991 (mmp) outliers start: 32 outliers final: 21 residues processed: 121 average time/residue: 0.4268 time to fit residues: 56.0288 Evaluate side-chains 122 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 23 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS B 202 ASN E 39 GLN E 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.167447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.137575 restraints weight = 11460.309| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.19 r_work: 0.3653 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8482 Z= 0.119 Angle : 0.548 9.199 11563 Z= 0.279 Chirality : 0.041 0.144 1346 Planarity : 0.005 0.057 1452 Dihedral : 6.796 83.173 1234 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.23 % Allowed : 25.24 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.25), residues: 1095 helix: 1.76 (0.27), residues: 373 sheet: -0.01 (0.32), residues: 261 loop : -0.96 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 137 TYR 0.014 0.001 TYR E 178 PHE 0.013 0.001 PHE C 151 TRP 0.019 0.002 TRP C 169 HIS 0.002 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8478) covalent geometry : angle 0.54830 (11555) SS BOND : bond 0.00488 ( 4) SS BOND : angle 0.71706 ( 8) hydrogen bonds : bond 0.03822 ( 419) hydrogen bonds : angle 4.69243 ( 1233) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.345 Fit side-chains REVERT: A 63 LYS cc_start: 0.3880 (OUTLIER) cc_final: 0.3263 (mmmm) REVERT: B 11 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7298 (tt0) REVERT: B 75 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7035 (mttt) REVERT: B 164 THR cc_start: 0.8854 (p) cc_final: 0.8649 (p) REVERT: B 221 ARG cc_start: 0.7926 (ttp-110) cc_final: 0.7536 (ptp-110) REVERT: C 262 MET cc_start: 0.8181 (mmm) cc_final: 0.7948 (tpp) REVERT: E 34 MET cc_start: 0.8272 (mmm) cc_final: 0.8040 (mmp) outliers start: 35 outliers final: 21 residues processed: 127 average time/residue: 0.4517 time to fit residues: 62.1196 Evaluate side-chains 121 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 84 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.166523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.136791 restraints weight = 11334.545| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.17 r_work: 0.3628 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8482 Z= 0.155 Angle : 0.586 8.905 11563 Z= 0.299 Chirality : 0.042 0.145 1346 Planarity : 0.005 0.052 1452 Dihedral : 6.784 83.235 1234 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.23 % Allowed : 25.00 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.25), residues: 1095 helix: 1.65 (0.27), residues: 373 sheet: -0.11 (0.32), residues: 258 loop : -0.96 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 148 TYR 0.015 0.001 TYR E 178 PHE 0.016 0.002 PHE C 151 TRP 0.018 0.002 TRP C 169 HIS 0.002 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 8478) covalent geometry : angle 0.58546 (11555) SS BOND : bond 0.00542 ( 4) SS BOND : angle 0.84336 ( 8) hydrogen bonds : bond 0.04216 ( 419) hydrogen bonds : angle 4.78853 ( 1233) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 103 time to evaluate : 0.349 Fit side-chains REVERT: A 63 LYS cc_start: 0.4099 (OUTLIER) cc_final: 0.3768 (mmmt) REVERT: B 11 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7236 (tt0) REVERT: B 75 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7066 (mttt) REVERT: B 221 ARG cc_start: 0.7928 (ttp-110) cc_final: 0.7508 (ptp-110) REVERT: C 262 MET cc_start: 0.8202 (mmm) cc_final: 0.7962 (tpp) REVERT: E 34 MET cc_start: 0.8272 (mmm) cc_final: 0.8008 (mmp) outliers start: 35 outliers final: 26 residues processed: 127 average time/residue: 0.4335 time to fit residues: 59.9552 Evaluate side-chains 125 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 48 optimal weight: 0.7980 chunk 91 optimal weight: 0.3980 chunk 49 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 45 optimal weight: 0.0980 chunk 12 optimal weight: 0.0570 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.169480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.140447 restraints weight = 11467.132| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.15 r_work: 0.3691 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8482 Z= 0.107 Angle : 0.544 9.517 11563 Z= 0.272 Chirality : 0.040 0.138 1346 Planarity : 0.004 0.050 1452 Dihedral : 6.635 76.109 1234 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.66 % Allowed : 26.69 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.25), residues: 1095 helix: 1.94 (0.27), residues: 373 sheet: 0.06 (0.31), residues: 261 loop : -0.85 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 148 TYR 0.011 0.001 TYR E 178 PHE 0.011 0.001 PHE C 151 TRP 0.019 0.002 TRP C 169 HIS 0.003 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 8478) covalent geometry : angle 0.54444 (11555) SS BOND : bond 0.00396 ( 4) SS BOND : angle 0.62449 ( 8) hydrogen bonds : bond 0.03524 ( 419) hydrogen bonds : angle 4.57971 ( 1233) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.304 Fit side-chains REVERT: B 221 ARG cc_start: 0.7879 (ttp-110) cc_final: 0.7490 (ptp-110) REVERT: E 93 MET cc_start: 0.8132 (ttp) cc_final: 0.7830 (ttp) outliers start: 22 outliers final: 17 residues processed: 114 average time/residue: 0.4791 time to fit residues: 59.0793 Evaluate side-chains 114 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 74 optimal weight: 1.9990 chunk 36 optimal weight: 0.0170 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 104 optimal weight: 0.2980 chunk 71 optimal weight: 3.9990 overall best weight: 1.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS B 202 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.166352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.137133 restraints weight = 11431.543| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.13 r_work: 0.3663 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8482 Z= 0.140 Angle : 0.574 9.513 11563 Z= 0.291 Chirality : 0.041 0.143 1346 Planarity : 0.004 0.051 1452 Dihedral : 6.657 76.756 1234 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.54 % Allowed : 27.29 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.25), residues: 1095 helix: 1.83 (0.27), residues: 373 sheet: -0.03 (0.31), residues: 264 loop : -0.83 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 148 TYR 0.015 0.001 TYR E 178 PHE 0.015 0.001 PHE C 151 TRP 0.017 0.002 TRP C 169 HIS 0.003 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8478) covalent geometry : angle 0.57353 (11555) SS BOND : bond 0.00506 ( 4) SS BOND : angle 0.77848 ( 8) hydrogen bonds : bond 0.03987 ( 419) hydrogen bonds : angle 4.68996 ( 1233) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.330 Fit side-chains REVERT: B 221 ARG cc_start: 0.7934 (ttp-110) cc_final: 0.7510 (ptp-110) REVERT: E 93 MET cc_start: 0.8208 (ttp) cc_final: 0.7960 (ttp) outliers start: 21 outliers final: 20 residues processed: 109 average time/residue: 0.4959 time to fit residues: 58.3149 Evaluate side-chains 116 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 61 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.167858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.138516 restraints weight = 11435.270| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.16 r_work: 0.3670 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8482 Z= 0.122 Angle : 0.554 9.441 11563 Z= 0.281 Chirality : 0.041 0.141 1346 Planarity : 0.004 0.051 1452 Dihedral : 6.575 71.860 1234 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.78 % Allowed : 27.05 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.25), residues: 1095 helix: 1.88 (0.27), residues: 373 sheet: -0.01 (0.31), residues: 262 loop : -0.82 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 148 TYR 0.013 0.001 TYR E 178 PHE 0.013 0.001 PHE C 151 TRP 0.019 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8478) covalent geometry : angle 0.55385 (11555) SS BOND : bond 0.00449 ( 4) SS BOND : angle 0.62400 ( 8) hydrogen bonds : bond 0.03802 ( 419) hydrogen bonds : angle 4.63114 ( 1233) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3426.80 seconds wall clock time: 59 minutes 11.57 seconds (3551.57 seconds total)