Starting phenix.real_space_refine on Sat Dec 28 10:29:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dwg_27753/12_2024/8dwg_27753.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dwg_27753/12_2024/8dwg_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_27753/12_2024/8dwg_27753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dwg_27753/12_2024/8dwg_27753.map" model { file = "/net/cci-nas-00/data/ceres_data/8dwg_27753/12_2024/8dwg_27753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dwg_27753/12_2024/8dwg_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-5532/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: 5.80, per 1000 atoms: 0.69 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: 2.42 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: 1.04 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: 2.91 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: 0.000 Normalize map: mean=0, sd=1: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.460 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:16.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.020 ------------------------------------------------------------------------------- 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 8537 Z= 0.343 Angle : 0.600 6.886 11619 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 *********************** 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 : 0.969 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: 1.1206 time to fit residues: 222.9226 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 : 1.016 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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 8537 Z= 0.189 Angle : 0.550 6.546 11619 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 *********************** 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 : 1.026 Fit side-chains REVERT: B 9 ASP cc_start: 0.7368 (m-30) cc_final: 0.7129 (m-30) REVERT: B 25 GLU cc_start: 0.7045 (tm-30) cc_final: 0.6606 (tm-30) REVERT: B 29 LYS cc_start: 0.7938 (mttp) cc_final: 0.7734 (mttp) REVERT: B 114 ASP cc_start: 0.7550 (t0) cc_final: 0.7152 (t0) REVERT: B 124 ASP cc_start: 0.6760 (t70) cc_final: 0.6542 (t70) REVERT: B 190 LYS cc_start: 0.7726 (tttt) cc_final: 0.7474 (ttpp) REVERT: B 196 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7202 (mm-30) REVERT: B 199 ASP cc_start: 0.6768 (p0) cc_final: 0.6480 (p0) REVERT: C 52 ARG cc_start: 0.7480 (mtt90) cc_final: 0.7265 (mtt90) REVERT: C 258 ASP cc_start: 0.6922 (t0) cc_final: 0.6370 (t0) REVERT: C 335 PHE cc_start: 0.8396 (m-80) cc_final: 0.8086 (m-80) REVERT: R 72 ASP cc_start: 0.7017 (m-30) cc_final: 0.6706 (m-30) REVERT: R 120 ARG cc_start: 0.8037 (ttp-170) cc_final: 0.7749 (ttm170) outliers start: 13 outliers final: 4 residues processed: 196 average time/residue: 1.2078 time to fit residues: 252.3138 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 : 0.976 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8537 Z= 0.294 Angle : 0.578 9.598 11619 Z= 0.308 Chirality : 0.043 0.174 1345 Planarity : 0.004 0.040 1456 Dihedral : 4.834 28.607 1199 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.93 % Allowed : 12.18 % Favored : 84.89 % 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: 0.80 (0.26), residues: 1081 helix: 1.96 (0.27), residues: 363 sheet: 0.59 (0.30), residues: 285 loop : -0.72 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 82 HIS 0.016 0.001 HIS B 82 PHE 0.019 0.002 PHE C 234 TYR 0.017 0.002 TYR E 178 ARG 0.008 0.001 ARG C 134 *********************** 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 207 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.986 Fit side-chains REVERT: B 9 ASP cc_start: 0.7411 (m-30) cc_final: 0.7127 (m-30) REVERT: B 25 GLU cc_start: 0.7049 (tm-30) cc_final: 0.6655 (tm-30) REVERT: B 114 ASP cc_start: 0.7571 (t0) cc_final: 0.7173 (t0) REVERT: B 124 ASP cc_start: 0.6796 (t70) cc_final: 0.6524 (t70) REVERT: B 196 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7212 (mm-30) REVERT: B 199 ASP cc_start: 0.6775 (p0) cc_final: 0.6496 (p0) REVERT: C 258 ASP cc_start: 0.6975 (t0) cc_final: 0.6422 (t0) REVERT: C 335 PHE cc_start: 0.8416 (m-80) cc_final: 0.8139 (m-80) REVERT: R 72 ASP cc_start: 0.7044 (m-30) cc_final: 0.6722 (m-30) REVERT: R 120 ARG cc_start: 0.8111 (ttp-170) cc_final: 0.7686 (ttm170) outliers start: 25 outliers final: 14 residues processed: 190 average time/residue: 1.1409 time to fit residues: 231.2960 Evaluate side-chains 184 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET 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 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 97 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** E 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8537 Z= 0.276 Angle : 0.562 6.947 11619 Z= 0.301 Chirality : 0.043 0.147 1345 Planarity : 0.004 0.037 1456 Dihedral : 4.717 26.261 1199 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.04 % Allowed : 13.82 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.93 (0.26), residues: 1081 helix: 2.25 (0.27), residues: 363 sheet: 0.53 (0.30), residues: 285 loop : -0.73 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 82 HIS 0.014 0.001 HIS B 82 PHE 0.015 0.002 PHE C 234 TYR 0.019 0.002 TYR C 105 ARG 0.008 0.000 ARG B 185 *********************** 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 201 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 1.022 Fit side-chains REVERT: B 25 GLU cc_start: 0.7060 (tm-30) cc_final: 0.6701 (tm-30) REVERT: B 114 ASP cc_start: 0.7535 (t0) cc_final: 0.7145 (t0) REVERT: B 124 ASP cc_start: 0.6749 (t70) cc_final: 0.6471 (t70) REVERT: B 196 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7207 (mm-30) REVERT: B 199 ASP cc_start: 0.6823 (p0) cc_final: 0.6506 (p0) REVERT: C 251 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8347 (mtt-85) REVERT: C 258 ASP cc_start: 0.6979 (t0) cc_final: 0.6450 (t0) REVERT: C 335 PHE cc_start: 0.8419 (m-80) cc_final: 0.8151 (m-80) REVERT: R 120 ARG cc_start: 0.8035 (ttp-170) cc_final: 0.7721 (ttm170) REVERT: R 156 LEU cc_start: 0.8183 (tm) cc_final: 0.7891 (tp) REVERT: R 160 LEU cc_start: 0.7913 (mt) cc_final: 0.7694 (mp) outliers start: 26 outliers final: 14 residues processed: 187 average time/residue: 1.1397 time to fit residues: 227.6937 Evaluate side-chains 187 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET 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 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 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 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.0470 chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8537 Z= 0.292 Angle : 0.564 6.169 11619 Z= 0.302 Chirality : 0.043 0.145 1345 Planarity : 0.004 0.037 1456 Dihedral : 4.717 25.532 1199 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.22 % Allowed : 13.58 % Favored : 82.20 % 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: 0.97 (0.26), residues: 1081 helix: 2.35 (0.27), residues: 363 sheet: 0.51 (0.30), residues: 285 loop : -0.73 (0.31), residues: 433 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 0.014 0.002 PHE C 234 TYR 0.023 0.002 TYR C 105 ARG 0.009 0.000 ARG B 185 *********************** 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: 36 poor density : 173 time to evaluate : 1.149 Fit side-chains REVERT: B 25 GLU cc_start: 0.7072 (tm-30) cc_final: 0.6744 (tm-30) REVERT: B 114 ASP cc_start: 0.7532 (t0) cc_final: 0.7147 (t0) REVERT: B 124 ASP cc_start: 0.6721 (OUTLIER) cc_final: 0.6438 (t70) REVERT: B 196 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7187 (mm-30) REVERT: B 199 ASP cc_start: 0.6828 (p0) cc_final: 0.6503 (p0) REVERT: C 251 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8340 (mtt-85) REVERT: C 258 ASP cc_start: 0.6974 (t0) cc_final: 0.6421 (t0) REVERT: C 335 PHE cc_start: 0.8452 (m-80) cc_final: 0.8221 (m-80) REVERT: D 38 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7257 (ttm) REVERT: R 120 ARG cc_start: 0.8003 (ttp-170) cc_final: 0.7688 (ttm170) REVERT: R 156 LEU cc_start: 0.8196 (tm) cc_final: 0.7849 (tp) REVERT: R 160 LEU cc_start: 0.7916 (mt) cc_final: 0.7680 (mp) outliers start: 36 outliers final: 19 residues processed: 191 average time/residue: 1.1811 time to fit residues: 240.4420 Evaluate side-chains 188 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 83 MET Chi-restraints excluded: chain B residue 124 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 D residue 38 MET 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 E residue 25 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 54 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: B 101 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8537 Z= 0.268 Angle : 0.552 6.205 11619 Z= 0.297 Chirality : 0.042 0.141 1345 Planarity : 0.004 0.036 1456 Dihedral : 4.651 25.126 1199 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.10 % Allowed : 14.29 % Favored : 81.62 % 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: 1.00 (0.26), residues: 1081 helix: 2.39 (0.28), residues: 363 sheet: 0.49 (0.30), residues: 285 loop : -0.70 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 82 HIS 0.005 0.001 HIS B 209 PHE 0.013 0.002 PHE R 104 TYR 0.020 0.002 TYR C 105 ARG 0.009 0.000 ARG B 185 *********************** 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 214 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 0.910 Fit side-chains REVERT: B 25 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6758 (tm-30) REVERT: B 76 VAL cc_start: 0.7539 (p) cc_final: 0.7298 (t) REVERT: B 114 ASP cc_start: 0.7540 (t0) cc_final: 0.7225 (t0) REVERT: B 124 ASP cc_start: 0.6721 (OUTLIER) cc_final: 0.6440 (t70) REVERT: B 196 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7182 (mm-30) REVERT: B 199 ASP cc_start: 0.6837 (p0) cc_final: 0.6514 (p0) REVERT: C 251 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8335 (mtt-85) REVERT: C 258 ASP cc_start: 0.6944 (t0) cc_final: 0.6381 (t0) REVERT: R 120 ARG cc_start: 0.7992 (ttp-170) cc_final: 0.7686 (ttm170) REVERT: R 156 LEU cc_start: 0.8207 (tm) cc_final: 0.7860 (tp) REVERT: R 160 LEU cc_start: 0.7918 (mt) cc_final: 0.7687 (mp) outliers start: 35 outliers final: 18 residues processed: 197 average time/residue: 1.0752 time to fit residues: 226.7647 Evaluate side-chains 196 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 124 ASP 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 25 SER 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 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 100 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8537 Z= 0.249 Angle : 0.543 6.503 11619 Z= 0.292 Chirality : 0.042 0.139 1345 Planarity : 0.004 0.036 1456 Dihedral : 4.607 25.339 1199 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.28 % Allowed : 15.69 % Favored : 81.03 % 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: 1.04 (0.26), residues: 1081 helix: 2.47 (0.28), residues: 364 sheet: 0.45 (0.30), residues: 285 loop : -0.69 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 82 HIS 0.004 0.001 HIS B 209 PHE 0.013 0.002 PHE R 104 TYR 0.016 0.002 TYR C 105 ARG 0.009 0.000 ARG B 185 *********************** 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 200 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 1.215 Fit side-chains REVERT: B 25 GLU cc_start: 0.7074 (tm-30) cc_final: 0.6755 (tm-30) REVERT: B 32 ARG cc_start: 0.7574 (mtm180) cc_final: 0.7312 (mtm180) REVERT: B 114 ASP cc_start: 0.7560 (t0) cc_final: 0.7218 (t0) REVERT: B 124 ASP cc_start: 0.6707 (OUTLIER) cc_final: 0.6419 (t70) REVERT: B 196 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7175 (mm-30) REVERT: B 199 ASP cc_start: 0.6835 (p0) cc_final: 0.6517 (p0) REVERT: C 251 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8334 (mtt-85) REVERT: C 258 ASP cc_start: 0.6963 (t0) cc_final: 0.6391 (t0) REVERT: C 335 PHE cc_start: 0.8367 (m-80) cc_final: 0.8022 (m-80) REVERT: R 120 ARG cc_start: 0.7983 (ttp-170) cc_final: 0.7760 (ttp-170) REVERT: R 156 LEU cc_start: 0.8213 (tm) cc_final: 0.7868 (tp) REVERT: R 160 LEU cc_start: 0.7918 (mt) cc_final: 0.7686 (mp) outliers start: 28 outliers final: 17 residues processed: 189 average time/residue: 1.1741 time to fit residues: 236.8056 Evaluate side-chains 189 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 124 ASP Chi-restraints excluded: chain C residue 31 SER 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 230 LEU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 39 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8537 Z= 0.239 Angle : 0.543 8.072 11619 Z= 0.291 Chirality : 0.042 0.139 1345 Planarity : 0.004 0.035 1456 Dihedral : 4.560 24.902 1199 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.81 % Allowed : 16.51 % Favored : 80.68 % 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: 1.03 (0.26), residues: 1081 helix: 2.48 (0.28), residues: 363 sheet: 0.45 (0.30), residues: 285 loop : -0.71 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 82 HIS 0.004 0.001 HIS B 209 PHE 0.014 0.001 PHE R 104 TYR 0.016 0.002 TYR E 178 ARG 0.009 0.000 ARG B 185 *********************** 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 198 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.926 Fit side-chains REVERT: B 25 GLU cc_start: 0.7086 (tm-30) cc_final: 0.6772 (tm-30) REVERT: B 32 ARG cc_start: 0.7537 (mtm180) cc_final: 0.7295 (mtm180) REVERT: B 114 ASP cc_start: 0.7548 (t0) cc_final: 0.7234 (t0) REVERT: B 124 ASP cc_start: 0.6700 (OUTLIER) cc_final: 0.6419 (t70) REVERT: B 196 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7210 (mm-30) REVERT: B 199 ASP cc_start: 0.6843 (p0) cc_final: 0.6524 (p0) REVERT: C 251 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8349 (mtt-85) REVERT: C 258 ASP cc_start: 0.6946 (t0) cc_final: 0.6328 (t0) REVERT: C 335 PHE cc_start: 0.8344 (m-80) cc_final: 0.8027 (m-80) REVERT: R 120 ARG cc_start: 0.7974 (ttp-170) cc_final: 0.7730 (ttp-170) REVERT: R 156 LEU cc_start: 0.8215 (tm) cc_final: 0.7889 (tp) REVERT: R 160 LEU cc_start: 0.7919 (mt) cc_final: 0.7717 (mp) REVERT: R 219 LEU cc_start: 0.8252 (mt) cc_final: 0.8012 (mm) REVERT: E 80 PHE cc_start: 0.8311 (m-80) cc_final: 0.8046 (m-80) outliers start: 24 outliers final: 15 residues processed: 189 average time/residue: 1.1809 time to fit residues: 238.3484 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 : 1.120 ------------------------------------------------------------------------------- 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 124 ASP 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 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 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 90 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 42 optimal weight: 0.0980 chunk 76 optimal weight: 0.6980 chunk 29 optimal weight: 0.0970 chunk 87 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8537 Z= 0.180 Angle : 0.524 9.855 11619 Z= 0.280 Chirality : 0.041 0.138 1345 Planarity : 0.004 0.034 1456 Dihedral : 4.374 24.139 1199 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.69 % Allowed : 16.86 % Favored : 80.44 % 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: 0.45 (0.30), residues: 284 loop : -0.68 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.003 0.001 HIS B 209 PHE 0.016 0.001 PHE R 104 TYR 0.016 0.001 TYR E 178 ARG 0.009 0.000 ARG B 185 *********************** 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 201 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 1.001 Fit side-chains REVERT: B 21 LYS cc_start: 0.8100 (ttpp) cc_final: 0.7840 (ttpp) REVERT: B 25 GLU cc_start: 0.7037 (tm-30) cc_final: 0.6702 (tm-30) REVERT: B 32 ARG cc_start: 0.7487 (mtm180) cc_final: 0.7265 (mtm180) REVERT: B 114 ASP cc_start: 0.7582 (t0) cc_final: 0.7310 (t0) REVERT: B 124 ASP cc_start: 0.6681 (OUTLIER) cc_final: 0.6400 (t70) REVERT: B 196 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7224 (mm-30) REVERT: B 199 ASP cc_start: 0.6843 (p0) cc_final: 0.6545 (p0) REVERT: B 232 LYS cc_start: 0.8012 (ttmm) cc_final: 0.7794 (ttmm) REVERT: C 49 ARG cc_start: 0.8619 (mmt-90) cc_final: 0.8399 (mmt-90) REVERT: C 251 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8340 (mtt-85) REVERT: C 258 ASP cc_start: 0.6922 (t0) cc_final: 0.6330 (t0) REVERT: C 335 PHE cc_start: 0.8339 (m-80) cc_final: 0.7987 (m-80) REVERT: R 120 ARG cc_start: 0.7945 (ttp-170) cc_final: 0.7702 (ttm170) REVERT: R 156 LEU cc_start: 0.8245 (tm) cc_final: 0.7878 (tp) REVERT: R 160 LEU cc_start: 0.7991 (mt) cc_final: 0.7716 (mp) REVERT: R 219 LEU cc_start: 0.8233 (mt) cc_final: 0.7968 (mm) REVERT: E 80 PHE cc_start: 0.8224 (m-80) cc_final: 0.7990 (m-80) outliers start: 23 outliers final: 18 residues processed: 192 average time/residue: 1.1647 time to fit residues: 238.6024 Evaluate side-chains 198 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 124 ASP 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 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 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 102 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 71 optimal weight: 0.4980 chunk 107 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 0.0170 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8537 Z= 0.223 Angle : 0.543 10.104 11619 Z= 0.289 Chirality : 0.042 0.137 1345 Planarity : 0.004 0.036 1456 Dihedral : 4.459 24.534 1199 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.22 % Allowed : 17.33 % Favored : 80.44 % 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: 1.12 (0.26), residues: 1081 helix: 2.64 (0.28), residues: 362 sheet: 0.44 (0.30), residues: 284 loop : -0.69 (0.30), residues: 435 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 0.013 0.001 PHE R 104 TYR 0.015 0.002 TYR E 178 ARG 0.009 0.000 ARG B 185 ********************** 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 196 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.996 Fit side-chains REVERT: B 25 GLU cc_start: 0.7034 (tm-30) cc_final: 0.6697 (tm-30) REVERT: B 32 ARG cc_start: 0.7503 (mtm180) cc_final: 0.7268 (mtm180) REVERT: B 114 ASP cc_start: 0.7580 (t0) cc_final: 0.7308 (t0) REVERT: B 124 ASP cc_start: 0.6687 (OUTLIER) cc_final: 0.6407 (t70) REVERT: B 196 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7217 (mm-30) REVERT: B 199 ASP cc_start: 0.6852 (p0) cc_final: 0.6537 (p0) REVERT: B 233 ASP cc_start: 0.7350 (t0) cc_final: 0.7080 (m-30) REVERT: C 49 ARG cc_start: 0.8597 (mmt-90) cc_final: 0.8387 (mmt-90) REVERT: C 251 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8326 (mtt-85) REVERT: C 258 ASP cc_start: 0.6906 (t0) cc_final: 0.6310 (t0) REVERT: C 335 PHE cc_start: 0.8336 (m-80) cc_final: 0.8020 (m-80) REVERT: R 120 ARG cc_start: 0.7950 (ttp-170) cc_final: 0.7722 (ttm170) REVERT: R 156 LEU cc_start: 0.8236 (tm) cc_final: 0.7875 (tp) REVERT: R 160 LEU cc_start: 0.7919 (mt) cc_final: 0.7689 (mp) REVERT: E 80 PHE cc_start: 0.8273 (m-80) cc_final: 0.8029 (m-80) outliers start: 19 outliers final: 16 residues processed: 190 average time/residue: 1.1496 time to fit residues: 233.0226 Evaluate side-chains 195 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 124 ASP 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 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 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 91 optimal weight: 0.7980 chunk 26 optimal weight: 0.0370 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.0470 chunk 75 optimal weight: 0.0010 overall best weight: 0.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN C 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.112623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.098427 restraints weight = 11823.461| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.63 r_work: 0.3187 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 8537 Z= 0.156 Angle : 0.514 12.657 11619 Z= 0.273 Chirality : 0.041 0.137 1345 Planarity : 0.004 0.036 1456 Dihedral : 4.267 24.454 1199 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.81 % Allowed : 16.98 % Favored : 80.21 % 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: 1.27 (0.27), residues: 1081 helix: 2.92 (0.28), residues: 356 sheet: 0.49 (0.30), residues: 284 loop : -0.68 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.003 0.001 HIS B 209 PHE 0.015 0.001 PHE R 104 TYR 0.015 0.001 TYR E 178 ARG 0.010 0.000 ARG B 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4019.39 seconds wall clock time: 72 minutes 41.16 seconds (4361.16 seconds total)