Starting phenix.real_space_refine on Sat Jul 26 02:23:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k20_61986/07_2025/9k20_61986.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k20_61986/07_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_61986/07_2025/9k20_61986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k20_61986/07_2025/9k20_61986.map" model { file = "/net/cci-nas-00/data/ceres_data/9k20_61986/07_2025/9k20_61986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k20_61986/07_2025/9k20_61986.cif" } resolution = 2.65 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= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'ARG:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'ASP: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, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 5} 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: {'GLN:plan1': 4, 'GLU:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 5, 'ARG:plan': 7} 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: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 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: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG: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: 5.38, per 1000 atoms: 0.65 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: 2.21 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.97 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: 3.41 Time building geometry restraints manager: 2.60 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: 3.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.140 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:15.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.710 ------------------------------------------------------------------------------- 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 (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: 0.07 (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 TRP 0.017 0.001 TRP A 99 HIS 0.003 0.001 HIS A 98 PHE 0.014 0.001 PHE A 113 TYR 0.017 0.001 TYR E 178 ARG 0.006 0.000 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.17751 ( 419) hydrogen bonds : angle 6.79217 ( 1233) SS BOND : bond 0.00417 ( 4) SS BOND : angle 0.38594 ( 8) covalent geometry : bond 0.00406 ( 8478) covalent geometry : angle 0.77714 (11555) *********************** 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 : 0.845 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: 1.0344 time to fit residues: 116.8015 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 : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 45 optimal weight: 0.0980 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 0.0980 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.170738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.142567 restraints weight = 11337.334| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.08 r_work: 0.3709 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8482 Z= 0.109 Angle : 0.524 6.738 11563 Z= 0.276 Chirality : 0.040 0.143 1346 Planarity : 0.005 0.058 1452 Dihedral : 6.576 89.447 1234 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.26 % Allowed : 23.31 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.45 (0.25), residues: 1095 helix: 1.52 (0.27), residues: 380 sheet: 0.37 (0.32), residues: 255 loop : -0.73 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 169 HIS 0.003 0.001 HIS C 91 PHE 0.010 0.001 PHE A 113 TYR 0.014 0.001 TYR E 178 ARG 0.003 0.000 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 419) hydrogen bonds : angle 4.91924 ( 1233) SS BOND : bond 0.00395 ( 4) SS BOND : angle 0.78253 ( 8) covalent geometry : bond 0.00226 ( 8478) covalent geometry : angle 0.52385 (11555) *********************** 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 134 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 1.007 Fit side-chains REVERT: B 11 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7377 (tt0) REVERT: C 220 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.8011 (mt0) REVERT: C 262 MET cc_start: 0.8307 (mmm) cc_final: 0.7991 (tpp) outliers start: 27 outliers final: 14 residues processed: 124 average time/residue: 0.9593 time to fit residues: 128.7999 Evaluate side-chains 110 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 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 C residue 147 SER Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 30 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 23 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS C 183 HIS C 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.165311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.135708 restraints weight = 11568.107| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.15 r_work: 0.3642 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8482 Z= 0.187 Angle : 0.593 7.453 11563 Z= 0.312 Chirality : 0.043 0.150 1346 Planarity : 0.005 0.053 1452 Dihedral : 6.819 87.512 1234 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.35 % Allowed : 22.34 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.32 (0.25), residues: 1095 helix: 1.37 (0.26), residues: 380 sheet: 0.24 (0.31), residues: 262 loop : -0.75 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 169 HIS 0.005 0.001 HIS A 98 PHE 0.019 0.002 PHE C 151 TYR 0.020 0.002 TYR E 178 ARG 0.002 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.04744 ( 419) hydrogen bonds : angle 4.99417 ( 1233) SS BOND : bond 0.00590 ( 4) SS BOND : angle 0.98972 ( 8) covalent geometry : bond 0.00427 ( 8478) covalent geometry : angle 0.59237 (11555) *********************** 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 141 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.971 Fit side-chains REVERT: A 203 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6577 (tp) REVERT: B 11 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: B 221 ARG cc_start: 0.7905 (ttp-110) cc_final: 0.7421 (ptp-110) REVERT: C 262 MET cc_start: 0.8314 (mmm) cc_final: 0.7926 (tpp) REVERT: E 34 MET cc_start: 0.8221 (mmm) cc_final: 0.8002 (mmp) outliers start: 36 outliers final: 18 residues processed: 126 average time/residue: 0.9147 time to fit residues: 125.3469 Evaluate side-chains 113 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 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 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 12 VAL Chi-restraints excluded: chain E residue 48 VAL 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 68 optimal weight: 0.0170 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.167668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.138283 restraints weight = 11435.461| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.15 r_work: 0.3658 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8482 Z= 0.133 Angle : 0.554 6.989 11563 Z= 0.286 Chirality : 0.041 0.146 1346 Planarity : 0.004 0.051 1452 Dihedral : 6.659 88.966 1234 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.86 % Allowed : 23.07 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.25), residues: 1095 helix: 1.53 (0.26), residues: 380 sheet: 0.23 (0.32), residues: 259 loop : -0.77 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.002 0.001 HIS A 74 PHE 0.015 0.001 PHE C 151 TYR 0.016 0.001 TYR E 178 ARG 0.002 0.000 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 419) hydrogen bonds : angle 4.79787 ( 1233) SS BOND : bond 0.00472 ( 4) SS BOND : angle 0.82485 ( 8) covalent geometry : bond 0.00293 ( 8478) covalent geometry : angle 0.55338 (11555) *********************** 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 131 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.948 Fit side-chains REVERT: A 203 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6595 (tp) REVERT: B 11 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7341 (tt0) REVERT: B 221 ARG cc_start: 0.7960 (ttp-110) cc_final: 0.7457 (ptp-110) REVERT: C 262 MET cc_start: 0.8203 (mmm) cc_final: 0.7876 (tpp) outliers start: 32 outliers final: 19 residues processed: 120 average time/residue: 0.8840 time to fit residues: 115.7704 Evaluate side-chains 113 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 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 127 CYS 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 246 ASP Chi-restraints excluded: chain C residue 274 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 75 optimal weight: 0.7980 chunk 4 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 83 optimal weight: 20.0000 chunk 68 optimal weight: 0.0870 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.170972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.142673 restraints weight = 11411.152| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.09 r_work: 0.3716 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8482 Z= 0.100 Angle : 0.513 7.660 11563 Z= 0.261 Chirality : 0.040 0.134 1346 Planarity : 0.004 0.049 1452 Dihedral : 6.366 83.945 1234 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.78 % Allowed : 24.40 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1095 helix: 1.95 (0.27), residues: 373 sheet: 0.31 (0.32), residues: 252 loop : -0.74 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 169 HIS 0.002 0.001 HIS E 35 PHE 0.010 0.001 PHE C 151 TYR 0.012 0.001 TYR E 178 ARG 0.003 0.000 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.03457 ( 419) hydrogen bonds : angle 4.49759 ( 1233) SS BOND : bond 0.00358 ( 4) SS BOND : angle 0.61492 ( 8) covalent geometry : bond 0.00206 ( 8478) covalent geometry : angle 0.51282 (11555) *********************** 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 127 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.884 Fit side-chains REVERT: B 93 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7296 (mmmt) REVERT: B 221 ARG cc_start: 0.7908 (ttp-110) cc_final: 0.7435 (ptp-110) REVERT: C 262 MET cc_start: 0.8159 (mmm) cc_final: 0.7926 (tpp) outliers start: 23 outliers final: 15 residues processed: 118 average time/residue: 0.9530 time to fit residues: 121.8983 Evaluate side-chains 113 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 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 93 LYS Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 146 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 47 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.168843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.139460 restraints weight = 11346.040| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.15 r_work: 0.3682 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8482 Z= 0.124 Angle : 0.546 7.489 11563 Z= 0.278 Chirality : 0.041 0.141 1346 Planarity : 0.004 0.050 1452 Dihedral : 6.675 87.460 1234 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.38 % Allowed : 24.76 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.25), residues: 1095 helix: 1.91 (0.27), residues: 373 sheet: 0.26 (0.31), residues: 260 loop : -0.70 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE C 151 TYR 0.016 0.001 TYR E 178 ARG 0.003 0.000 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 419) hydrogen bonds : angle 4.55214 ( 1233) SS BOND : bond 0.00415 ( 4) SS BOND : angle 0.80759 ( 8) covalent geometry : bond 0.00273 ( 8478) covalent geometry : angle 0.54608 (11555) *********************** 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 127 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.958 Fit side-chains REVERT: B 11 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7389 (tt0) REVERT: B 93 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7357 (mmmt) REVERT: C 262 MET cc_start: 0.8141 (mmm) cc_final: 0.7895 (tpp) outliers start: 28 outliers final: 20 residues processed: 117 average time/residue: 0.9117 time to fit residues: 115.8502 Evaluate side-chains 117 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 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 93 LYS 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 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 246 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 86 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 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 = 0.4092 r_free = 0.4092 target = 0.168775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.140219 restraints weight = 11466.792| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.11 r_work: 0.3681 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8482 Z= 0.121 Angle : 0.538 7.302 11563 Z= 0.274 Chirality : 0.040 0.140 1346 Planarity : 0.004 0.050 1452 Dihedral : 6.686 87.125 1234 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.26 % Allowed : 25.00 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1095 helix: 1.93 (0.27), residues: 373 sheet: 0.27 (0.31), residues: 260 loop : -0.70 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE C 151 TYR 0.015 0.001 TYR E 178 ARG 0.003 0.000 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 419) hydrogen bonds : angle 4.54235 ( 1233) SS BOND : bond 0.00413 ( 4) SS BOND : angle 0.67877 ( 8) covalent geometry : bond 0.00265 ( 8478) covalent geometry : angle 0.53778 (11555) *********************** 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 128 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.865 Fit side-chains REVERT: B 93 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7364 (mmmt) REVERT: B 221 ARG cc_start: 0.7799 (ttp-110) cc_final: 0.7429 (ptp-110) REVERT: C 262 MET cc_start: 0.8161 (mmm) cc_final: 0.7937 (tpp) REVERT: E 34 MET cc_start: 0.8178 (mmm) cc_final: 0.7913 (mmp) REVERT: E 93 MET cc_start: 0.8193 (ttp) cc_final: 0.7891 (ttp) outliers start: 27 outliers final: 19 residues processed: 116 average time/residue: 0.9648 time to fit residues: 121.0676 Evaluate side-chains 115 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 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 93 LYS 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 50 optimal weight: 30.0000 chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 24 optimal weight: 0.1980 chunk 15 optimal weight: 0.2980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 HIS B 202 ASN C 340 ASN E 39 GLN E 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.167250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.138612 restraints weight = 11503.166| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.10 r_work: 0.3663 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1451 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= 0.145 Angle : 0.563 7.515 11563 Z= 0.289 Chirality : 0.041 0.145 1346 Planarity : 0.004 0.050 1452 Dihedral : 6.737 86.809 1234 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.26 % Allowed : 25.24 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.55 (0.25), residues: 1095 helix: 1.84 (0.27), residues: 373 sheet: 0.22 (0.32), residues: 261 loop : -0.75 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.016 0.002 PHE E 68 TYR 0.017 0.001 TYR E 178 ARG 0.003 0.000 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.04062 ( 419) hydrogen bonds : angle 4.62819 ( 1233) SS BOND : bond 0.00461 ( 4) SS BOND : angle 0.82684 ( 8) covalent geometry : bond 0.00326 ( 8478) covalent geometry : angle 0.56306 (11555) *********************** 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 127 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.988 Fit side-chains REVERT: B 11 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.6975 (tm-30) REVERT: B 93 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7362 (mmmt) REVERT: B 221 ARG cc_start: 0.7842 (ttp-110) cc_final: 0.7429 (ptp-110) REVERT: C 262 MET cc_start: 0.8153 (mmm) cc_final: 0.7905 (tpp) REVERT: E 34 MET cc_start: 0.8192 (mmm) cc_final: 0.7943 (mmp) outliers start: 27 outliers final: 22 residues processed: 116 average time/residue: 0.9558 time to fit residues: 120.4804 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 : 0.882 ------------------------------------------------------------------------------- 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 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 93 LYS 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 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 246 ASP Chi-restraints excluded: chain C residue 274 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 19 optimal weight: 0.0670 chunk 37 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN C 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.167523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.138132 restraints weight = 11488.017| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.16 r_work: 0.3663 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1495 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= 0.138 Angle : 0.568 9.413 11563 Z= 0.287 Chirality : 0.041 0.142 1346 Planarity : 0.005 0.084 1452 Dihedral : 6.764 86.298 1234 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.02 % Allowed : 25.36 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.52 (0.25), residues: 1095 helix: 1.84 (0.27), residues: 373 sheet: 0.19 (0.31), residues: 261 loop : -0.78 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.032 0.002 PHE E 68 TYR 0.016 0.001 TYR E 178 ARG 0.003 0.000 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 419) hydrogen bonds : angle 4.63098 ( 1233) SS BOND : bond 0.00469 ( 4) SS BOND : angle 0.79963 ( 8) covalent geometry : bond 0.00307 ( 8478) covalent geometry : angle 0.56748 (11555) *********************** 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 128 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.887 Fit side-chains REVERT: B 11 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.6980 (tm-30) REVERT: B 93 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7368 (mmmt) REVERT: B 221 ARG cc_start: 0.7932 (ttp-110) cc_final: 0.7506 (ptp-110) REVERT: C 262 MET cc_start: 0.8178 (mmm) cc_final: 0.7945 (tpp) REVERT: E 34 MET cc_start: 0.8192 (mmm) cc_final: 0.7947 (mmp) outliers start: 25 outliers final: 21 residues processed: 119 average time/residue: 0.9317 time to fit residues: 120.3755 Evaluate side-chains 125 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 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 93 LYS 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 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 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 59 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 54 optimal weight: 0.0980 chunk 61 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.168388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.139892 restraints weight = 11526.993| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.11 r_work: 0.3678 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8482 Z= 0.120 Angle : 0.545 9.512 11563 Z= 0.277 Chirality : 0.040 0.141 1346 Planarity : 0.004 0.068 1452 Dihedral : 6.747 86.060 1234 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.66 % Allowed : 25.85 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.25), residues: 1095 helix: 1.94 (0.27), residues: 373 sheet: 0.24 (0.31), residues: 259 loop : -0.78 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 169 HIS 0.002 0.001 HIS E 35 PHE 0.036 0.001 PHE E 68 TYR 0.015 0.001 TYR E 178 ARG 0.004 0.000 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 419) hydrogen bonds : angle 4.53606 ( 1233) SS BOND : bond 0.00411 ( 4) SS BOND : angle 0.72240 ( 8) covalent geometry : bond 0.00261 ( 8478) covalent geometry : angle 0.54463 (11555) ********************** 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 118 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.872 Fit side-chains REVERT: B 11 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.6953 (tm-30) REVERT: B 93 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7389 (mmmt) REVERT: B 221 ARG cc_start: 0.7927 (ttp-110) cc_final: 0.7494 (ptp-110) REVERT: C 262 MET cc_start: 0.8142 (mmm) cc_final: 0.7922 (tpp) outliers start: 22 outliers final: 19 residues processed: 110 average time/residue: 0.9531 time to fit residues: 113.2721 Evaluate side-chains 117 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 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 93 LYS 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 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 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 73 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.168370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.139754 restraints weight = 11556.444| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.12 r_work: 0.3675 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8482 Z= 0.122 Angle : 0.550 9.487 11563 Z= 0.279 Chirality : 0.041 0.141 1346 Planarity : 0.004 0.061 1452 Dihedral : 6.750 86.615 1234 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.90 % Allowed : 25.72 % 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 (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: 0.59 (0.25), residues: 1095 helix: 1.94 (0.27), residues: 373 sheet: 0.20 (0.31), residues: 260 loop : -0.77 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.028 0.001 PHE E 68 TYR 0.015 0.001 TYR E 178 ARG 0.004 0.000 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 419) hydrogen bonds : angle 4.56264 ( 1233) SS BOND : bond 0.00419 ( 4) SS BOND : angle 0.65686 ( 8) covalent geometry : bond 0.00268 ( 8478) covalent geometry : angle 0.54966 (11555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7268.08 seconds wall clock time: 127 minutes 29.93 seconds (7649.93 seconds total)