Starting phenix.real_space_refine on Sat Jun 7 00:18:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dwg_27753/06_2025/8dwg_27753.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dwg_27753/06_2025/8dwg_27753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dwg_27753/06_2025/8dwg_27753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dwg_27753/06_2025/8dwg_27753.map" model { file = "/net/cci-nas-00/data/ceres_data/8dwg_27753/06_2025/8dwg_27753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dwg_27753/06_2025/8dwg_27753.cif" } resolution = 2.71 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5356 2.51 5 N 1421 2.21 5 O 1516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8350 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 124 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 11} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1704 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2480 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 92 Chain: "D" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 350 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1937 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 240} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1730 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'U39': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.60, per 1000 atoms: 0.67 Number of scatterers: 8350 At special positions: 0 Unit cell: (97.68, 116.16, 120.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1516 8.00 N 1421 7.00 C 5356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 251 " distance=2.03 Simple disulfide: pdb=" SG CYS R 161 " - pdb=" SG CYS R 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2060 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 37.7% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.536A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.875A pdb=" N ILE B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 131 through 135 removed outlier: 4.055A pdb=" N ARG B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 removed outlier: 3.637A pdb=" N GLU B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 removed outlier: 4.436A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 removed outlier: 3.736A pdb=" N ALA B 168 " --> pdb=" O PRO B 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 183 through 204 removed outlier: 3.574A pdb=" N ALA B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 removed outlier: 3.537A pdb=" N TYR B 243 " --> pdb=" O ASN B 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 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 12 through 24 removed outlier: 3.664A pdb=" N VAL D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'R' and resid 24 through 53 removed outlier: 3.904A pdb=" N LEU R 28 " --> pdb=" O TYR R 24 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER R 29 " --> pdb=" O LYS R 25 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL R 47 " --> pdb=" O THR R 43 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL R 48 " --> pdb=" O GLY R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 88 removed outlier: 3.754A pdb=" N TYR R 64 " --> pdb=" O ALA R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 98 removed outlier: 3.738A pdb=" N LYS R 96 " --> pdb=" O HIS R 92 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE R 97 " --> pdb=" O THR R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 126 removed outlier: 4.801A pdb=" N PHE R 104 " --> pdb=" O PRO R 100 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 133 Processing helix chain 'R' and resid 137 through 161 Processing helix chain 'R' and resid 170 through 204 Processing helix chain 'R' and resid 212 through 229 Processing helix chain 'R' and resid 230 through 239 removed outlier: 6.192A pdb=" N PHE R 236 " --> pdb=" O PHE R 232 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE R 237 " --> pdb=" O GLY R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 266 removed outlier: 3.541A pdb=" N LEU R 249 " --> pdb=" O ASP R 245 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE R 250 " --> pdb=" O ARG R 246 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL R 253 " --> pdb=" O LEU R 249 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LEU R 255 " --> pdb=" O CYS R 251 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL R 256 " --> pdb=" O HIS R 252 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 273 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.015A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 72 through 76 removed outlier: 9.552A pdb=" N ALA B 105 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.393A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.804A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.967A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.882A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.822A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.560A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.537A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.578A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.578A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.696A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.46 Time building geometry restraints manager: 2.66 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: 2668 1.34 - 1.46: 1972 1.46 - 1.58: 3819 1.58 - 1.69: 1 1.69 - 1.81: 77 Bond restraints: 8537 Sorted by residual: bond pdb=" C11 U39 R 401 " pdb=" N2 U39 R 401 " ideal model delta sigma weight residual 1.433 1.379 0.054 2.00e-02 2.50e+03 7.16e+00 bond pdb=" N2 U39 R 401 " pdb=" S1 U39 R 401 " ideal model delta sigma weight residual 1.671 1.627 0.044 2.00e-02 2.50e+03 4.77e+00 bond pdb=" C SER C 67 " pdb=" N ARG C 68 " ideal model delta sigma weight residual 1.332 1.302 0.030 1.40e-02 5.10e+03 4.71e+00 bond pdb=" CB VAL B 109 " pdb=" CG1 VAL B 109 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.55e+00 bond pdb=" CG PRO E 224 " pdb=" CD PRO E 224 " ideal model delta sigma weight residual 1.512 1.481 0.031 2.70e-02 1.37e+03 1.35e+00 ... (remaining 8532 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 11180 1.38 - 2.75: 356 2.75 - 4.13: 61 4.13 - 5.51: 17 5.51 - 6.89: 5 Bond angle restraints: 11619 Sorted by residual: angle pdb=" N MET E 180 " pdb=" CA MET E 180 " pdb=" CB MET E 180 " ideal model delta sigma weight residual 114.17 108.46 5.71 1.14e+00 7.69e-01 2.51e+01 angle pdb=" N LEU R 230 " pdb=" CA LEU R 230 " pdb=" C LEU R 230 " ideal model delta sigma weight residual 109.81 116.34 -6.53 2.21e+00 2.05e-01 8.72e+00 angle pdb=" C HIS R 243 " pdb=" N VAL R 244 " pdb=" CA VAL R 244 " ideal model delta sigma weight residual 122.97 120.08 2.89 9.80e-01 1.04e+00 8.72e+00 angle pdb=" C THR B 216 " pdb=" N CYS B 217 " pdb=" CA CYS B 217 " ideal model delta sigma weight residual 121.54 116.12 5.42 1.91e+00 2.74e-01 8.06e+00 angle pdb=" N PHE C 234 " pdb=" CA PHE C 234 " pdb=" C PHE C 234 " ideal model delta sigma weight residual 110.50 114.36 -3.86 1.41e+00 5.03e-01 7.51e+00 ... (remaining 11614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 4570 17.46 - 34.92: 337 34.92 - 52.37: 58 52.37 - 69.83: 4 69.83 - 87.29: 4 Dihedral angle restraints: 4973 sinusoidal: 1783 harmonic: 3190 Sorted by residual: dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 141.76 -48.76 1 1.00e+01 1.00e-02 3.27e+01 dihedral pdb=" CA MET E 128 " pdb=" C MET E 128 " pdb=" N THR E 129 " pdb=" CA THR E 129 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA PHE C 234 " pdb=" C PHE C 234 " pdb=" N PHE C 235 " pdb=" CA PHE C 235 " ideal model delta harmonic sigma weight residual 180.00 158.89 21.11 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 4970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 911 0.041 - 0.081: 333 0.081 - 0.122: 84 0.122 - 0.162: 14 0.162 - 0.203: 3 Chirality restraints: 1345 Sorted by residual: chirality pdb=" CG LEU B 143 " pdb=" CB LEU B 143 " pdb=" CD1 LEU B 143 " pdb=" CD2 LEU B 143 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB THR C 223 " pdb=" CA THR C 223 " pdb=" OG1 THR C 223 " pdb=" CG2 THR C 223 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.06e-01 chirality pdb=" CG LEU R 191 " pdb=" CB LEU R 191 " pdb=" CD1 LEU R 191 " pdb=" CD2 LEU R 191 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.71e-01 ... (remaining 1342 not shown) Planarity restraints: 1456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U39 R 401 " -0.058 2.00e-02 2.50e+03 9.95e-02 1.24e+02 pdb=" C10 U39 R 401 " 0.094 2.00e-02 2.50e+03 pdb=" C2 U39 R 401 " 0.119 2.00e-02 2.50e+03 pdb=" N1 U39 R 401 " -0.152 2.00e-02 2.50e+03 pdb=" O1 U39 R 401 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 48 " -0.037 5.00e-02 4.00e+02 5.63e-02 5.08e+00 pdb=" N PRO D 49 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 48 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" C ASP D 48 " 0.034 2.00e-02 2.50e+03 pdb=" O ASP D 48 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO D 49 " -0.012 2.00e-02 2.50e+03 ... (remaining 1453 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 127 2.66 - 3.22: 7656 3.22 - 3.78: 12658 3.78 - 4.34: 18081 4.34 - 4.90: 30416 Nonbonded interactions: 68938 Sorted by model distance: nonbonded pdb=" OH TYR R 106 " pdb=" O PHE R 232 " model vdw 2.106 3.040 nonbonded pdb=" OG SER C 281 " pdb=" OD2 ASP D 48 " model vdw 2.177 3.040 nonbonded pdb=" OH TYR B 243 " pdb=" OH TYR R 130 " model vdw 2.177 3.040 nonbonded pdb=" OE2 GLU B 25 " pdb=" NZ LYS B 29 " model vdw 2.199 3.120 nonbonded pdb=" O TYR B 170 " pdb=" NH1 ARG B 188 " model vdw 2.227 3.120 ... (remaining 68933 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: 0.010 Normalize map: mean=0, sd=1: 1.680 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.400 Find NCS groups from input model: 0.110 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:14.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8540 Z= 0.225 Angle : 0.600 6.886 11625 Z= 0.341 Chirality : 0.045 0.203 1345 Planarity : 0.005 0.100 1456 Dihedral : 12.585 87.290 2904 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.25), residues: 1081 helix: -1.23 (0.24), residues: 367 sheet: 0.27 (0.31), residues: 281 loop : -0.85 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 339 HIS 0.013 0.001 HIS B 82 PHE 0.012 0.002 PHE R 225 TYR 0.016 0.002 TYR C 59 ARG 0.009 0.000 ARG C 49 Details of bonding type rmsd hydrogen bonds : bond 0.24512 ( 428) hydrogen bonds : angle 8.67372 ( 1212) SS BOND : bond 0.00614 ( 3) SS BOND : angle 0.77789 ( 6) covalent geometry : bond 0.00524 ( 8537) covalent geometry : angle 0.59983 (11619) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.927 Fit side-chains REVERT: B 20 ASP cc_start: 0.7590 (m-30) cc_final: 0.7338 (m-30) REVERT: B 25 GLU cc_start: 0.6932 (tm-30) cc_final: 0.6186 (tm-30) REVERT: B 29 LYS cc_start: 0.7546 (mttp) cc_final: 0.7309 (mttp) REVERT: B 114 ASP cc_start: 0.7540 (t0) cc_final: 0.7099 (t0) REVERT: B 196 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7204 (mm-30) REVERT: C 258 ASP cc_start: 0.6638 (t0) cc_final: 0.6086 (t0) REVERT: R 72 ASP cc_start: 0.7025 (m-30) cc_final: 0.6711 (m-30) REVERT: R 77 SER cc_start: 0.8207 (p) cc_final: 0.7966 (p) REVERT: R 156 LEU cc_start: 0.8166 (tp) cc_final: 0.7951 (tp) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 1.0745 time to fit residues: 213.8980 Evaluate side-chains 181 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0040 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 0.0570 chunk 43 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 0.2980 overall best weight: 0.3510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 80 ASN ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 144 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 ASN C 340 ASN E 39 GLN E 167 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.114548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.099883 restraints weight = 11479.402| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.64 r_work: 0.3177 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8540 Z= 0.133 Angle : 0.550 6.546 11625 Z= 0.300 Chirality : 0.042 0.146 1345 Planarity : 0.004 0.046 1456 Dihedral : 4.861 31.751 1199 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.52 % Allowed : 8.67 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1081 helix: 1.32 (0.27), residues: 366 sheet: 0.64 (0.31), residues: 277 loop : -0.73 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 82 HIS 0.013 0.001 HIS B 82 PHE 0.017 0.001 PHE R 104 TYR 0.021 0.001 TYR E 178 ARG 0.005 0.000 ARG C 49 Details of bonding type rmsd hydrogen bonds : bond 0.05278 ( 428) hydrogen bonds : angle 5.06914 ( 1212) SS BOND : bond 0.00537 ( 3) SS BOND : angle 0.49015 ( 6) covalent geometry : bond 0.00289 ( 8537) covalent geometry : angle 0.55017 (11619) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 0.947 Fit side-chains REVERT: B 9 ASP cc_start: 0.7920 (m-30) cc_final: 0.7682 (m-30) REVERT: B 25 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7347 (tm-30) REVERT: B 29 LYS cc_start: 0.8484 (mttp) cc_final: 0.8252 (mttp) REVERT: B 114 ASP cc_start: 0.7894 (t0) cc_final: 0.7461 (t0) REVERT: B 190 LYS cc_start: 0.7990 (tttt) cc_final: 0.7759 (ttpp) REVERT: B 196 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7770 (mm-30) REVERT: B 199 ASP cc_start: 0.7202 (p0) cc_final: 0.6907 (p0) REVERT: C 52 ARG cc_start: 0.8162 (mtt90) cc_final: 0.7959 (mtt90) REVERT: C 258 ASP cc_start: 0.7489 (t0) cc_final: 0.6914 (t0) REVERT: C 335 PHE cc_start: 0.8575 (m-80) cc_final: 0.8308 (m-80) REVERT: R 72 ASP cc_start: 0.7547 (m-30) cc_final: 0.7252 (m-30) REVERT: R 120 ARG cc_start: 0.8345 (ttp-170) cc_final: 0.8081 (ttm170) outliers start: 13 outliers final: 4 residues processed: 196 average time/residue: 1.2122 time to fit residues: 252.9645 Evaluate side-chains 190 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 186 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 84 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 0.0270 chunk 87 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 80 ASN ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 130 ASN B 144 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 130 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.112339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097774 restraints weight = 11613.990| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.64 r_work: 0.3137 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8540 Z= 0.233 Angle : 0.607 9.558 11625 Z= 0.323 Chirality : 0.045 0.170 1345 Planarity : 0.005 0.041 1456 Dihedral : 4.953 28.422 1199 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.04 % Allowed : 12.18 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.26), residues: 1081 helix: 1.83 (0.27), residues: 363 sheet: 0.58 (0.30), residues: 285 loop : -0.74 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 147 HIS 0.017 0.002 HIS B 82 PHE 0.020 0.002 PHE C 234 TYR 0.020 0.002 TYR C 105 ARG 0.008 0.001 ARG B 185 Details of bonding type rmsd hydrogen bonds : bond 0.05318 ( 428) hydrogen bonds : angle 4.90439 ( 1212) SS BOND : bond 0.00715 ( 3) SS BOND : angle 0.46941 ( 6) covalent geometry : bond 0.00551 ( 8537) covalent geometry : angle 0.60708 (11619) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.930 Fit side-chains REVERT: B 9 ASP cc_start: 0.7994 (m-30) cc_final: 0.7704 (m-30) REVERT: B 25 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7409 (tm-30) REVERT: B 29 LYS cc_start: 0.8473 (mttp) cc_final: 0.8219 (mttp) REVERT: B 114 ASP cc_start: 0.7922 (t0) cc_final: 0.7494 (t0) REVERT: B 143 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7868 (mm) REVERT: B 196 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7761 (mm-30) REVERT: B 199 ASP cc_start: 0.7221 (p0) cc_final: 0.6913 (p0) REVERT: C 258 ASP cc_start: 0.7523 (t0) cc_final: 0.6946 (t0) REVERT: R 72 ASP cc_start: 0.7564 (m-30) cc_final: 0.7264 (m-30) REVERT: R 120 ARG cc_start: 0.8432 (ttp-170) cc_final: 0.8135 (ttm170) REVERT: E 55 SER cc_start: 0.8395 (OUTLIER) cc_final: 0.8135 (p) outliers start: 26 outliers final: 15 residues processed: 188 average time/residue: 1.1830 time to fit residues: 236.8415 Evaluate side-chains 191 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 5 optimal weight: 0.0040 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS B 101 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.113554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.098898 restraints weight = 11582.608| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.68 r_work: 0.3155 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8540 Z= 0.154 Angle : 0.542 6.995 11625 Z= 0.291 Chirality : 0.042 0.147 1345 Planarity : 0.004 0.036 1456 Dihedral : 4.665 27.037 1199 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.16 % Allowed : 13.58 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.26), residues: 1081 helix: 2.28 (0.28), residues: 363 sheet: 0.52 (0.30), residues: 284 loop : -0.72 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 82 HIS 0.013 0.001 HIS B 82 PHE 0.014 0.001 PHE C 234 TYR 0.016 0.002 TYR E 178 ARG 0.008 0.000 ARG B 185 Details of bonding type rmsd hydrogen bonds : bond 0.04426 ( 428) hydrogen bonds : angle 4.62042 ( 1212) SS BOND : bond 0.00570 ( 3) SS BOND : angle 0.40438 ( 6) covalent geometry : bond 0.00355 ( 8537) covalent geometry : angle 0.54192 (11619) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 1.024 Fit side-chains REVERT: B 9 ASP cc_start: 0.8020 (m-30) cc_final: 0.7689 (m-30) REVERT: B 25 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7427 (tm-30) REVERT: B 29 LYS cc_start: 0.8484 (mttp) cc_final: 0.8158 (mttp) REVERT: B 114 ASP cc_start: 0.7892 (t0) cc_final: 0.7456 (t0) REVERT: B 143 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7716 (mm) REVERT: B 196 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7726 (mm-30) REVERT: B 199 ASP cc_start: 0.7249 (p0) cc_final: 0.6949 (p0) REVERT: C 52 ARG cc_start: 0.8215 (mtt90) cc_final: 0.8012 (mtt90) REVERT: C 251 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8545 (mtt-85) REVERT: C 258 ASP cc_start: 0.7521 (t0) cc_final: 0.6953 (t0) REVERT: C 335 PHE cc_start: 0.8560 (m-80) cc_final: 0.8138 (m-80) REVERT: D 38 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8141 (ttm) REVERT: R 72 ASP cc_start: 0.7618 (m-30) cc_final: 0.7299 (m-30) REVERT: R 120 ARG cc_start: 0.8390 (ttp-170) cc_final: 0.8016 (ttm170) REVERT: R 156 LEU cc_start: 0.8486 (tm) cc_final: 0.8159 (tt) REVERT: R 160 LEU cc_start: 0.8248 (mt) cc_final: 0.7992 (mp) outliers start: 27 outliers final: 13 residues processed: 186 average time/residue: 1.7275 time to fit residues: 344.1961 Evaluate side-chains 187 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain R residue 35 CYS Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 104 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 102 optimal weight: 0.0030 chunk 94 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 60 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN ** B 223 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 = 0.3496 r_free = 0.3496 target = 0.114000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.099410 restraints weight = 11494.216| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.65 r_work: 0.3172 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8540 Z= 0.135 Angle : 0.517 5.824 11625 Z= 0.279 Chirality : 0.041 0.140 1345 Planarity : 0.004 0.034 1456 Dihedral : 4.491 26.257 1199 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.28 % Allowed : 14.75 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1081 helix: 2.54 (0.28), residues: 363 sheet: 0.51 (0.30), residues: 284 loop : -0.70 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 PHE 0.014 0.001 PHE R 104 TYR 0.016 0.001 TYR E 178 ARG 0.009 0.000 ARG B 185 Details of bonding type rmsd hydrogen bonds : bond 0.04117 ( 428) hydrogen bonds : angle 4.47811 ( 1212) SS BOND : bond 0.00507 ( 3) SS BOND : angle 0.34060 ( 6) covalent geometry : bond 0.00308 ( 8537) covalent geometry : angle 0.51667 (11619) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 0.973 Fit side-chains REVERT: B 25 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7447 (tm-30) REVERT: B 29 LYS cc_start: 0.8455 (mttp) cc_final: 0.8153 (mttp) REVERT: B 114 ASP cc_start: 0.7888 (t0) cc_final: 0.7499 (t0) REVERT: B 143 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7780 (mm) REVERT: B 196 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7715 (mm-30) REVERT: B 199 ASP cc_start: 0.7275 (p0) cc_final: 0.6972 (p0) REVERT: C 251 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8571 (mtt-85) REVERT: C 258 ASP cc_start: 0.7478 (t0) cc_final: 0.6898 (t0) REVERT: C 335 PHE cc_start: 0.8508 (m-80) cc_final: 0.8177 (m-80) REVERT: D 38 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8146 (ttm) REVERT: R 120 ARG cc_start: 0.8303 (ttp-170) cc_final: 0.8086 (ttp-170) REVERT: R 156 LEU cc_start: 0.8488 (tm) cc_final: 0.8182 (tp) REVERT: R 160 LEU cc_start: 0.8247 (mt) cc_final: 0.7988 (mp) outliers start: 28 outliers final: 12 residues processed: 197 average time/residue: 1.2416 time to fit residues: 261.2494 Evaluate side-chains 194 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain R residue 35 CYS Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN C 220 GLN E 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.109990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.095785 restraints weight = 11686.438| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.61 r_work: 0.3129 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8540 Z= 0.206 Angle : 0.571 6.970 11625 Z= 0.306 Chirality : 0.043 0.144 1345 Planarity : 0.004 0.037 1456 Dihedral : 4.688 25.412 1199 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.75 % Allowed : 15.69 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 1081 helix: 2.39 (0.28), residues: 363 sheet: 0.47 (0.30), residues: 285 loop : -0.70 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 147 HIS 0.005 0.001 HIS E 35 PHE 0.015 0.002 PHE R 75 TYR 0.023 0.002 TYR C 105 ARG 0.008 0.001 ARG B 185 Details of bonding type rmsd hydrogen bonds : bond 0.04666 ( 428) hydrogen bonds : angle 4.63584 ( 1212) SS BOND : bond 0.00607 ( 3) SS BOND : angle 0.39766 ( 6) covalent geometry : bond 0.00487 ( 8537) covalent geometry : angle 0.57058 (11619) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.871 Fit side-chains REVERT: B 25 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7471 (tm-30) REVERT: B 29 LYS cc_start: 0.8501 (mttp) cc_final: 0.8197 (mttp) REVERT: B 76 VAL cc_start: 0.7766 (p) cc_final: 0.7503 (t) REVERT: B 114 ASP cc_start: 0.7899 (t0) cc_final: 0.7510 (t0) REVERT: B 196 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7740 (mm-30) REVERT: B 199 ASP cc_start: 0.7287 (p0) cc_final: 0.6959 (p0) REVERT: C 251 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8545 (mtt-85) REVERT: C 258 ASP cc_start: 0.7504 (t0) cc_final: 0.6908 (t0) REVERT: C 335 PHE cc_start: 0.8527 (m-80) cc_final: 0.8091 (m-80) REVERT: R 156 LEU cc_start: 0.8497 (tm) cc_final: 0.8190 (tp) REVERT: R 160 LEU cc_start: 0.8221 (mt) cc_final: 0.7997 (mp) REVERT: E 55 SER cc_start: 0.8351 (OUTLIER) cc_final: 0.8094 (p) outliers start: 32 outliers final: 16 residues processed: 199 average time/residue: 1.1024 time to fit residues: 235.3926 Evaluate side-chains 191 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain R residue 35 CYS Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 98 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 0.0370 chunk 97 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN ** B 223 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 = 0.3460 r_free = 0.3460 target = 0.110326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.096041 restraints weight = 11716.514| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.62 r_work: 0.3135 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8540 Z= 0.175 Angle : 0.552 6.616 11625 Z= 0.296 Chirality : 0.043 0.154 1345 Planarity : 0.004 0.036 1456 Dihedral : 4.615 24.397 1199 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.93 % Allowed : 17.21 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1081 helix: 2.45 (0.28), residues: 364 sheet: 0.44 (0.30), residues: 285 loop : -0.71 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 82 HIS 0.005 0.001 HIS B 209 PHE 0.013 0.002 PHE R 104 TYR 0.018 0.002 TYR C 105 ARG 0.009 0.000 ARG B 185 Details of bonding type rmsd hydrogen bonds : bond 0.04420 ( 428) hydrogen bonds : angle 4.57404 ( 1212) SS BOND : bond 0.00570 ( 3) SS BOND : angle 0.37143 ( 6) covalent geometry : bond 0.00410 ( 8537) covalent geometry : angle 0.55248 (11619) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.865 Fit side-chains REVERT: B 25 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7512 (tm-30) REVERT: B 29 LYS cc_start: 0.8497 (mttp) cc_final: 0.8219 (mttp) REVERT: B 114 ASP cc_start: 0.7904 (t0) cc_final: 0.7575 (t0) REVERT: B 196 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7783 (mm-30) REVERT: B 199 ASP cc_start: 0.7303 (p0) cc_final: 0.6986 (p0) REVERT: C 251 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8544 (mtt-85) REVERT: C 258 ASP cc_start: 0.7506 (t0) cc_final: 0.6917 (t0) REVERT: C 335 PHE cc_start: 0.8524 (m-80) cc_final: 0.8204 (m-80) REVERT: R 156 LEU cc_start: 0.8507 (tm) cc_final: 0.8187 (tp) REVERT: R 160 LEU cc_start: 0.8223 (mt) cc_final: 0.7998 (mp) outliers start: 25 outliers final: 15 residues processed: 188 average time/residue: 1.1480 time to fit residues: 230.2314 Evaluate side-chains 191 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain R residue 35 CYS Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 11 optimal weight: 0.8980 chunk 99 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 107 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN C 220 GLN C 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.111140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.096902 restraints weight = 11903.775| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.63 r_work: 0.3159 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8540 Z= 0.141 Angle : 0.528 6.954 11625 Z= 0.283 Chirality : 0.042 0.139 1345 Planarity : 0.004 0.034 1456 Dihedral : 4.463 23.785 1199 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.46 % Allowed : 18.15 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1081 helix: 2.57 (0.28), residues: 362 sheet: 0.43 (0.30), residues: 284 loop : -0.70 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 PHE 0.015 0.001 PHE R 104 TYR 0.015 0.002 TYR E 178 ARG 0.009 0.000 ARG B 185 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 428) hydrogen bonds : angle 4.47927 ( 1212) SS BOND : bond 0.00516 ( 3) SS BOND : angle 0.34331 ( 6) covalent geometry : bond 0.00323 ( 8537) covalent geometry : angle 0.52832 (11619) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.987 Fit side-chains REVERT: B 25 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7457 (tm-30) REVERT: B 29 LYS cc_start: 0.8466 (mttp) cc_final: 0.8179 (mttp) REVERT: B 114 ASP cc_start: 0.7919 (t0) cc_final: 0.7559 (t0) REVERT: B 196 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7782 (mm-30) REVERT: B 199 ASP cc_start: 0.7298 (p0) cc_final: 0.6989 (p0) REVERT: C 251 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8561 (mtt-85) REVERT: C 258 ASP cc_start: 0.7507 (t0) cc_final: 0.6896 (t0) REVERT: C 335 PHE cc_start: 0.8514 (m-80) cc_final: 0.8160 (m-80) REVERT: R 156 LEU cc_start: 0.8502 (tm) cc_final: 0.8166 (tp) REVERT: R 160 LEU cc_start: 0.8213 (mt) cc_final: 0.7968 (mp) REVERT: R 219 LEU cc_start: 0.8362 (mt) cc_final: 0.8136 (mm) REVERT: E 148 ARG cc_start: 0.7983 (ptt90) cc_final: 0.7719 (ttp80) outliers start: 21 outliers final: 14 residues processed: 185 average time/residue: 1.1302 time to fit residues: 223.2848 Evaluate side-chains 188 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain R residue 35 CYS Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 5 optimal weight: 0.0040 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.114137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.099903 restraints weight = 11838.759| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.63 r_work: 0.3167 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8540 Z= 0.122 Angle : 0.517 9.661 11625 Z= 0.276 Chirality : 0.041 0.138 1345 Planarity : 0.004 0.034 1456 Dihedral : 4.376 24.648 1199 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.22 % Allowed : 18.27 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.26), residues: 1081 helix: 2.67 (0.28), residues: 362 sheet: 0.40 (0.30), residues: 289 loop : -0.65 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 PHE 0.014 0.001 PHE R 104 TYR 0.015 0.001 TYR E 178 ARG 0.009 0.000 ARG B 185 Details of bonding type rmsd hydrogen bonds : bond 0.03852 ( 428) hydrogen bonds : angle 4.38548 ( 1212) SS BOND : bond 0.00467 ( 3) SS BOND : angle 0.34035 ( 6) covalent geometry : bond 0.00276 ( 8537) covalent geometry : angle 0.51701 (11619) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.895 Fit side-chains REVERT: B 21 LYS cc_start: 0.8488 (ttpp) cc_final: 0.8249 (ttpp) REVERT: B 25 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7419 (tm-30) REVERT: B 29 LYS cc_start: 0.8449 (mttp) cc_final: 0.8155 (mttp) REVERT: B 114 ASP cc_start: 0.7892 (t0) cc_final: 0.7572 (t0) REVERT: B 196 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7772 (mm-30) REVERT: B 199 ASP cc_start: 0.7277 (p0) cc_final: 0.6970 (p0) REVERT: C 251 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8568 (mtt-85) REVERT: C 258 ASP cc_start: 0.7468 (t0) cc_final: 0.6839 (t0) REVERT: C 335 PHE cc_start: 0.8501 (m-80) cc_final: 0.8145 (m-80) REVERT: R 156 LEU cc_start: 0.8530 (tm) cc_final: 0.8194 (tp) REVERT: R 160 LEU cc_start: 0.8281 (mt) cc_final: 0.8004 (mp) REVERT: R 219 LEU cc_start: 0.8351 (mt) cc_final: 0.8130 (mm) REVERT: E 148 ARG cc_start: 0.7964 (ptt90) cc_final: 0.7707 (ttp80) outliers start: 19 outliers final: 16 residues processed: 190 average time/residue: 1.0963 time to fit residues: 222.3584 Evaluate side-chains 193 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain R residue 35 CYS Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 27 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 103 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN R 133 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.111375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.097176 restraints weight = 11837.045| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.63 r_work: 0.3156 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8540 Z= 0.141 Angle : 0.537 9.595 11625 Z= 0.285 Chirality : 0.042 0.140 1345 Planarity : 0.004 0.034 1456 Dihedral : 4.429 23.959 1199 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.22 % Allowed : 18.27 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.26), residues: 1081 helix: 2.77 (0.28), residues: 356 sheet: 0.38 (0.30), residues: 289 loop : -0.70 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 PHE 0.014 0.001 PHE R 104 TYR 0.014 0.002 TYR E 178 ARG 0.009 0.000 ARG B 185 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 428) hydrogen bonds : angle 4.42257 ( 1212) SS BOND : bond 0.00504 ( 3) SS BOND : angle 0.34759 ( 6) covalent geometry : bond 0.00324 ( 8537) covalent geometry : angle 0.53688 (11619) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 2.065 Fit side-chains REVERT: B 25 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7425 (tm-30) REVERT: B 29 LYS cc_start: 0.8437 (mttp) cc_final: 0.8148 (mttp) REVERT: B 196 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7733 (mm-30) REVERT: B 199 ASP cc_start: 0.7284 (p0) cc_final: 0.6976 (p0) REVERT: C 251 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8537 (mtt-85) REVERT: C 258 ASP cc_start: 0.7468 (t0) cc_final: 0.6880 (t0) REVERT: C 335 PHE cc_start: 0.8503 (m-80) cc_final: 0.8133 (m-80) REVERT: D 38 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8134 (ttm) REVERT: R 156 LEU cc_start: 0.8523 (tm) cc_final: 0.8185 (tp) REVERT: R 160 LEU cc_start: 0.8218 (mt) cc_final: 0.7951 (mp) REVERT: R 219 LEU cc_start: 0.8360 (mt) cc_final: 0.8134 (mm) REVERT: E 148 ARG cc_start: 0.7962 (ptt90) cc_final: 0.7714 (ttp80) outliers start: 19 outliers final: 15 residues processed: 192 average time/residue: 1.7138 time to fit residues: 351.0444 Evaluate side-chains 195 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain R residue 35 CYS Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 13 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 68 optimal weight: 0.0670 chunk 32 optimal weight: 0.0050 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.4332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.112004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.097718 restraints weight = 11937.087| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.64 r_work: 0.3164 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8540 Z= 0.125 Angle : 0.528 12.937 11625 Z= 0.279 Chirality : 0.041 0.136 1345 Planarity : 0.004 0.035 1456 Dihedral : 4.369 24.217 1199 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.22 % Allowed : 18.27 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.26), residues: 1081 helix: 2.84 (0.28), residues: 356 sheet: 0.41 (0.30), residues: 289 loop : -0.68 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 PHE 0.014 0.001 PHE R 104 TYR 0.015 0.001 TYR E 178 ARG 0.009 0.000 ARG B 185 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 428) hydrogen bonds : angle 4.37611 ( 1212) SS BOND : bond 0.00459 ( 3) SS BOND : angle 0.34199 ( 6) covalent geometry : bond 0.00283 ( 8537) covalent geometry : angle 0.52840 (11619) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8185.41 seconds wall clock time: 144 minutes 53.69 seconds (8693.69 seconds total)