Starting phenix.real_space_refine on Wed Mar 12 16:16:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s8l_24896/03_2025/7s8l_24896.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s8l_24896/03_2025/7s8l_24896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s8l_24896/03_2025/7s8l_24896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s8l_24896/03_2025/7s8l_24896.map" model { file = "/net/cci-nas-00/data/ceres_data/7s8l_24896/03_2025/7s8l_24896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s8l_24896/03_2025/7s8l_24896.cif" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5244 2.51 5 N 1388 2.21 5 O 1492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8177 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1862 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 7, 'TRANS': 242} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 8, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 93 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 56 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 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: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2475 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 88 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: "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 Time building chain proxies: 5.89, per 1000 atoms: 0.72 Number of scatterers: 8177 At special positions: 0 Unit cell: (90.09, 122.85, 126.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1492 8.00 N 1388 7.00 C 5244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " 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: 1.97 Conformation dependent library (CDL) restraints added in 1.2 seconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2042 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 37.5% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'R' and resid 30 through 57 removed outlier: 3.854A pdb=" N VAL R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY R 47 " --> pdb=" O VAL R 43 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE R 57 " --> pdb=" O TRP R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 95 removed outlier: 3.826A pdb=" N VAL R 68 " --> pdb=" O PHE R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 133 removed outlier: 3.881A pdb=" N LEU R 120 " --> pdb=" O GLY R 116 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER R 121 " --> pdb=" O LEU R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 140 Processing helix chain 'R' and resid 144 through 167 removed outlier: 3.712A pdb=" N PHE R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 211 Processing helix chain 'R' and resid 219 through 245 Proline residue: R 238 - end of helix Processing helix chain 'R' and resid 245 through 250 Processing helix chain 'R' and resid 256 through 280 Proline residue: R 262 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'B' and resid 6 through 31 Processing helix chain 'B' and resid 45 through 49 removed outlier: 4.045A pdb=" N ILE B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 99 removed outlier: 3.718A pdb=" N GLN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) 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: 4.070A pdb=" N ARG B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.698A pdb=" N LEU B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 164 through 170 removed outlier: 3.582A pdb=" N ALA B 168 " --> pdb=" O PRO B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 202 Processing helix chain 'B' and resid 223 through 243 removed outlier: 3.876A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 22 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.916A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN C 132 " --> pdb=" O ARG C 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 128 through 132' Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.701A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.572A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 removed outlier: 4.136A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.512A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.932A 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: 3.995A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.462A 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: 3.865A pdb=" N ARG C 46 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.899A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.934A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.824A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N CYS C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR C 179 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU C 168 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 175 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.945A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.776A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.922A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.560A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.988A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR E 115 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.410A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.410A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 143 through 148 411 hydrogen bonds defined for protein. 1149 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: 2.33 Time building geometry restraints manager: 2.36 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: 2623 1.34 - 1.46: 2027 1.46 - 1.58: 3631 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 8353 Sorted by residual: bond pdb=" N CYS B 217 " pdb=" CA CYS B 217 " ideal model delta sigma weight residual 1.459 1.492 -0.033 9.10e-03 1.21e+04 1.32e+01 bond pdb=" N VAL B 219 " pdb=" CA VAL B 219 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.23e+00 bond pdb=" N THR B 216 " pdb=" CA THR B 216 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.44e-02 4.82e+03 6.62e+00 bond pdb=" N ALA B 218 " pdb=" CA ALA B 218 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.37e-02 5.33e+03 6.14e+00 bond pdb=" N ASP B 220 " pdb=" CA ASP B 220 " ideal model delta sigma weight residual 1.455 1.487 -0.031 1.30e-02 5.92e+03 5.77e+00 ... (remaining 8348 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 11155 1.66 - 3.32: 183 3.32 - 4.98: 31 4.98 - 6.64: 3 6.64 - 8.29: 1 Bond angle restraints: 11373 Sorted by residual: angle pdb=" CA THR B 216 " pdb=" C THR B 216 " pdb=" O THR B 216 " ideal model delta sigma weight residual 121.49 117.46 4.03 1.16e+00 7.43e-01 1.21e+01 angle pdb=" CA CYS B 217 " pdb=" C CYS B 217 " pdb=" O CYS B 217 " ideal model delta sigma weight residual 119.08 116.08 3.00 1.05e+00 9.07e-01 8.17e+00 angle pdb=" N THR B 221 " pdb=" CA THR B 221 " pdb=" C THR B 221 " ideal model delta sigma weight residual 113.61 109.60 4.01 1.50e+00 4.44e-01 7.13e+00 angle pdb=" N LEU R 237 " pdb=" CA LEU R 237 " pdb=" C LEU R 237 " ideal model delta sigma weight residual 109.81 115.53 -5.72 2.21e+00 2.05e-01 6.70e+00 angle pdb=" C GLY E 197 " pdb=" N THR E 198 " pdb=" CA THR E 198 " ideal model delta sigma weight residual 121.54 126.36 -4.82 1.91e+00 2.74e-01 6.37e+00 ... (remaining 11368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 4376 15.06 - 30.12: 369 30.12 - 45.17: 90 45.17 - 60.23: 15 60.23 - 75.29: 3 Dihedral angle restraints: 4853 sinusoidal: 1691 harmonic: 3162 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 93.00 141.50 -48.50 1 1.00e+01 1.00e-02 3.24e+01 dihedral pdb=" CA ARG E 179 " pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta harmonic sigma weight residual 180.00 161.89 18.11 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ASP B 199 " pdb=" C ASP B 199 " pdb=" N ILE B 200 " pdb=" CA ILE B 200 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 4850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 979 0.042 - 0.083: 249 0.083 - 0.125: 94 0.125 - 0.166: 6 0.166 - 0.208: 1 Chirality restraints: 1329 Sorted by residual: chirality pdb=" CA VAL B 219 " pdb=" N VAL B 219 " pdb=" C VAL B 219 " pdb=" CB VAL B 219 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA LEU R 237 " pdb=" N LEU R 237 " pdb=" C LEU R 237 " pdb=" CB LEU R 237 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA ILE E 177 " pdb=" N ILE E 177 " pdb=" C ILE E 177 " pdb=" CB ILE E 177 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 1326 not shown) Planarity restraints: 1430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 233 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C LEU R 233 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU R 233 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU R 234 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 172 " -0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO E 173 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO E 173 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 173 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 48 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" CG ASP D 48 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASP D 48 " -0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP D 48 " -0.009 2.00e-02 2.50e+03 ... (remaining 1427 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1369 2.77 - 3.30: 7110 3.30 - 3.84: 12625 3.84 - 4.37: 14156 4.37 - 4.90: 26477 Nonbonded interactions: 61737 Sorted by model distance: nonbonded pdb=" ND2 ASN R 48 " pdb=" OD2 ASP R 75 " model vdw 2.238 3.120 nonbonded pdb=" OD1 ASP R 75 " pdb=" OG SER R 272 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR R 113 " pdb=" O GLY R 236 " model vdw 2.324 3.040 nonbonded pdb=" O ASP C 163 " pdb=" OG1 THR C 164 " model vdw 2.333 3.040 nonbonded pdb=" O TYR B 170 " pdb=" NH1 ARG B 188 " model vdw 2.340 3.120 ... (remaining 61732 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: 1.780 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.400 Find NCS groups from input model: 0.100 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:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 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 : 0.003 0.037 8353 Z= 0.177 Angle : 0.558 8.294 11373 Z= 0.317 Chirality : 0.042 0.208 1329 Planarity : 0.003 0.039 1430 Dihedral : 12.220 75.290 2805 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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 (0.26), residues: 1074 helix: 3.16 (0.28), residues: 352 sheet: 0.62 (0.31), residues: 267 loop : -0.94 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 190 HIS 0.004 0.001 HIS C 54 PHE 0.017 0.001 PHE R 81 TYR 0.010 0.001 TYR E 178 ARG 0.008 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.802 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 177 average time/residue: 1.1829 time to fit residues: 222.3117 Evaluate side-chains 165 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 278 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.0570 chunk 84 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 48 ASN B 116 ASN B 144 ASN C 35 ASN C 239 ASN E 159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.119744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.106064 restraints weight = 10915.673| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.48 r_work: 0.3345 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8353 Z= 0.258 Angle : 0.612 6.264 11373 Z= 0.330 Chirality : 0.044 0.145 1329 Planarity : 0.004 0.046 1430 Dihedral : 4.251 18.728 1168 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.31 % Allowed : 9.72 % Favored : 87.97 % 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: 1.20 (0.26), residues: 1074 helix: 2.98 (0.28), residues: 355 sheet: 0.73 (0.30), residues: 272 loop : -1.05 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP R 190 HIS 0.006 0.001 HIS E 35 PHE 0.013 0.002 PHE C 151 TYR 0.015 0.002 TYR E 178 ARG 0.007 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.824 Fit side-chains REVERT: R 280 PHE cc_start: 0.8422 (t80) cc_final: 0.8207 (t80) REVERT: B 73 LYS cc_start: 0.8742 (mttp) cc_final: 0.8541 (mttm) REVERT: B 101 ASN cc_start: 0.8124 (t0) cc_final: 0.7686 (t0) outliers start: 19 outliers final: 9 residues processed: 173 average time/residue: 1.1850 time to fit residues: 217.6017 Evaluate side-chains 174 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 275 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 0.5980 chunk 39 optimal weight: 0.0370 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN C 35 ASN C 75 GLN C 220 GLN C 268 ASN E 159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.121628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.107896 restraints weight = 11156.511| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.49 r_work: 0.3373 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8353 Z= 0.166 Angle : 0.524 5.785 11373 Z= 0.284 Chirality : 0.041 0.151 1329 Planarity : 0.004 0.044 1430 Dihedral : 3.996 18.770 1168 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.07 % Allowed : 12.03 % Favored : 85.91 % 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: 1.37 (0.26), residues: 1074 helix: 3.18 (0.28), residues: 355 sheet: 0.77 (0.31), residues: 279 loop : -0.98 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 190 HIS 0.004 0.001 HIS E 35 PHE 0.009 0.001 PHE C 151 TYR 0.015 0.001 TYR E 178 ARG 0.008 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.826 Fit side-chains REVERT: R 280 PHE cc_start: 0.8408 (t80) cc_final: 0.8199 (t80) REVERT: B 73 LYS cc_start: 0.8731 (mttp) cc_final: 0.8491 (mttp) REVERT: C 304 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.8021 (mtm180) REVERT: C 312 ASP cc_start: 0.7666 (t0) cc_final: 0.7428 (t0) outliers start: 17 outliers final: 9 residues processed: 173 average time/residue: 1.1609 time to fit residues: 213.0597 Evaluate side-chains 177 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 304 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 18 optimal weight: 0.0060 chunk 27 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 64 optimal weight: 3.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN C 75 GLN C 220 GLN E 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.121958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.108298 restraints weight = 11078.768| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.48 r_work: 0.3379 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8353 Z= 0.161 Angle : 0.510 5.779 11373 Z= 0.276 Chirality : 0.041 0.152 1329 Planarity : 0.004 0.042 1430 Dihedral : 3.919 18.490 1168 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.19 % Allowed : 14.09 % Favored : 83.72 % 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: 1.41 (0.26), residues: 1074 helix: 3.25 (0.28), residues: 355 sheet: 0.78 (0.30), residues: 281 loop : -0.99 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 190 HIS 0.004 0.001 HIS E 35 PHE 0.011 0.001 PHE R 81 TYR 0.014 0.001 TYR E 178 ARG 0.005 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.815 Fit side-chains REVERT: B 73 LYS cc_start: 0.8732 (mttp) cc_final: 0.8508 (mttp) REVERT: C 304 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8025 (mtm180) REVERT: C 312 ASP cc_start: 0.7678 (t0) cc_final: 0.7448 (t0) outliers start: 18 outliers final: 9 residues processed: 168 average time/residue: 1.1312 time to fit residues: 201.8198 Evaluate side-chains 174 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 164 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 304 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 68 optimal weight: 0.0060 chunk 106 optimal weight: 2.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 116 ASN B 244 ASN E 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.120667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.107125 restraints weight = 11010.172| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.47 r_work: 0.3361 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8353 Z= 0.189 Angle : 0.534 5.726 11373 Z= 0.289 Chirality : 0.042 0.152 1329 Planarity : 0.004 0.044 1430 Dihedral : 3.993 18.818 1168 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.92 % Allowed : 13.49 % Favored : 83.60 % 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: 1.39 (0.26), residues: 1074 helix: 3.23 (0.28), residues: 355 sheet: 0.82 (0.30), residues: 281 loop : -1.03 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 190 HIS 0.005 0.001 HIS E 35 PHE 0.011 0.001 PHE C 234 TYR 0.012 0.001 TYR E 178 ARG 0.003 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.917 Fit side-chains REVERT: B 73 LYS cc_start: 0.8726 (mttp) cc_final: 0.8469 (mttp) REVERT: C 22 ARG cc_start: 0.8039 (ptm160) cc_final: 0.7837 (ttp-170) REVERT: C 304 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8025 (mtm180) REVERT: C 312 ASP cc_start: 0.7704 (t0) cc_final: 0.7459 (t0) outliers start: 24 outliers final: 10 residues processed: 173 average time/residue: 1.1387 time to fit residues: 209.2658 Evaluate side-chains 179 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 66 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 27 optimal weight: 0.0170 chunk 89 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 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 116 ASN B 244 ASN C 75 GLN E 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.121180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.107474 restraints weight = 11033.103| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.48 r_work: 0.3366 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8353 Z= 0.180 Angle : 0.535 9.768 11373 Z= 0.288 Chirality : 0.042 0.217 1329 Planarity : 0.004 0.044 1430 Dihedral : 4.058 24.080 1168 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.92 % Allowed : 13.85 % Favored : 83.23 % 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: 1.40 (0.26), residues: 1074 helix: 3.27 (0.27), residues: 353 sheet: 0.82 (0.30), residues: 281 loop : -1.04 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 63 HIS 0.004 0.001 HIS E 35 PHE 0.011 0.001 PHE R 81 TYR 0.012 0.001 TYR E 178 ARG 0.003 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.945 Fit side-chains REVERT: B 73 LYS cc_start: 0.8721 (mttp) cc_final: 0.8517 (mttp) REVERT: C 22 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7828 (ttp-170) REVERT: C 304 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8011 (mtm180) REVERT: C 312 ASP cc_start: 0.7695 (t0) cc_final: 0.7450 (t0) REVERT: E 128 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7170 (mtm) outliers start: 24 outliers final: 14 residues processed: 175 average time/residue: 1.1192 time to fit residues: 208.2470 Evaluate side-chains 181 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 76 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 58 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 116 ASN B 229 ASN B 244 ASN C 88 ASN E 159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.120786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.107074 restraints weight = 10974.940| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.47 r_work: 0.3358 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8353 Z= 0.190 Angle : 0.545 8.262 11373 Z= 0.294 Chirality : 0.042 0.203 1329 Planarity : 0.004 0.044 1430 Dihedral : 4.099 24.957 1168 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.79 % Allowed : 14.46 % Favored : 82.75 % 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: 1.42 (0.26), residues: 1074 helix: 3.26 (0.27), residues: 353 sheet: 0.90 (0.30), residues: 275 loop : -1.03 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 63 HIS 0.005 0.001 HIS E 35 PHE 0.011 0.001 PHE C 151 TYR 0.013 0.001 TYR E 178 ARG 0.003 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.879 Fit side-chains REVERT: R 280 PHE cc_start: 0.8412 (t80) cc_final: 0.8182 (t80) REVERT: C 22 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7828 (ttp-170) REVERT: C 304 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8012 (mtm180) REVERT: C 312 ASP cc_start: 0.7710 (t0) cc_final: 0.7460 (t0) REVERT: E 128 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7279 (mtm) outliers start: 23 outliers final: 14 residues processed: 174 average time/residue: 1.1253 time to fit residues: 208.1884 Evaluate side-chains 183 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 201 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 77 optimal weight: 0.0770 chunk 74 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 116 ASN B 244 ASN C 75 GLN E 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.118293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.104757 restraints weight = 11037.810| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.48 r_work: 0.3321 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 8353 Z= 0.279 Angle : 0.619 8.270 11373 Z= 0.333 Chirality : 0.045 0.209 1329 Planarity : 0.004 0.049 1430 Dihedral : 4.407 28.034 1168 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.92 % Allowed : 14.70 % Favored : 82.38 % 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 (0.26), residues: 1074 helix: 3.06 (0.28), residues: 353 sheet: 0.86 (0.30), residues: 279 loop : -1.10 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 63 HIS 0.007 0.001 HIS E 35 PHE 0.015 0.002 PHE C 234 TYR 0.015 0.002 TYR B 163 ARG 0.003 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.807 Fit side-chains REVERT: R 280 PHE cc_start: 0.8440 (t80) cc_final: 0.8199 (t80) REVERT: C 61 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8402 (ppp) REVERT: C 304 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8027 (mtm180) REVERT: C 312 ASP cc_start: 0.7747 (t0) cc_final: 0.7492 (t0) REVERT: E 128 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7455 (mtm) outliers start: 24 outliers final: 16 residues processed: 175 average time/residue: 1.1109 time to fit residues: 206.4190 Evaluate side-chains 184 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 201 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 33 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS B 116 ASN B 244 ASN C 237 ASN E 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.119848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.106138 restraints weight = 11251.914| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.50 r_work: 0.3342 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8353 Z= 0.213 Angle : 0.567 7.616 11373 Z= 0.308 Chirality : 0.043 0.196 1329 Planarity : 0.004 0.048 1430 Dihedral : 4.236 25.615 1166 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.55 % Allowed : 15.55 % Favored : 81.90 % 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: 1.35 (0.26), residues: 1074 helix: 3.14 (0.28), residues: 353 sheet: 0.99 (0.30), residues: 272 loop : -1.10 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 190 HIS 0.005 0.001 HIS E 35 PHE 0.012 0.001 PHE C 151 TYR 0.013 0.001 TYR B 163 ARG 0.003 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.882 Fit side-chains REVERT: R 280 PHE cc_start: 0.8427 (t80) cc_final: 0.8198 (t80) REVERT: C 22 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7682 (ptm160) REVERT: C 304 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8024 (mtm180) REVERT: C 312 ASP cc_start: 0.7739 (t0) cc_final: 0.7492 (t0) REVERT: E 128 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.7273 (mtm) outliers start: 21 outliers final: 14 residues processed: 173 average time/residue: 1.2337 time to fit residues: 226.6871 Evaluate side-chains 180 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 14 optimal weight: 0.0770 chunk 104 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 0.0060 chunk 86 optimal weight: 0.0050 chunk 5 optimal weight: 0.7980 chunk 81 optimal weight: 0.0010 chunk 44 optimal weight: 0.0670 chunk 34 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 overall best weight: 0.0312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN C 32 GLN C 75 GLN C 237 ASN E 35 HIS E 159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.128705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.114846 restraints weight = 11249.163| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.49 r_work: 0.3478 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8353 Z= 0.119 Angle : 0.464 6.582 11373 Z= 0.252 Chirality : 0.040 0.168 1329 Planarity : 0.004 0.040 1430 Dihedral : 3.647 18.780 1166 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.97 % Allowed : 17.38 % Favored : 81.65 % 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: 1.64 (0.26), residues: 1074 helix: 3.41 (0.27), residues: 351 sheet: 1.08 (0.30), residues: 283 loop : -0.94 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 190 HIS 0.003 0.001 HIS B 209 PHE 0.018 0.001 PHE R 81 TYR 0.015 0.001 TYR E 178 ARG 0.005 0.000 ARG B 132 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 161 time to evaluate : 0.997 Fit side-chains REVERT: C 234 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.7706 (t80) outliers start: 8 outliers final: 3 residues processed: 167 average time/residue: 1.3839 time to fit residues: 244.6350 Evaluate side-chains 157 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 153 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.0010 chunk 80 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 83 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.0870 overall best weight: 0.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN C 32 GLN C 54 HIS C 75 GLN E 159 ASN E 171 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.124776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.110865 restraints weight = 11229.801| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.49 r_work: 0.3416 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8353 Z= 0.151 Angle : 0.524 11.218 11373 Z= 0.281 Chirality : 0.041 0.161 1329 Planarity : 0.004 0.050 1430 Dihedral : 3.743 21.191 1166 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.73 % Allowed : 19.32 % Favored : 79.95 % 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: 1.74 (0.26), residues: 1074 helix: 3.50 (0.27), residues: 353 sheet: 1.06 (0.30), residues: 282 loop : -0.83 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 63 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE R 244 TYR 0.013 0.001 TYR E 178 ARG 0.013 0.000 ARG B 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7772.63 seconds wall clock time: 135 minutes 20.39 seconds (8120.39 seconds total)