Starting phenix.real_space_refine on Wed Feb 12 15:45:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s8l_24896/02_2025/7s8l_24896.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s8l_24896/02_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_24896/02_2025/7s8l_24896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s8l_24896/02_2025/7s8l_24896.map" model { file = "/net/cci-nas-00/data/ceres_data/7s8l_24896/02_2025/7s8l_24896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s8l_24896/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.93, per 1000 atoms: 0.60 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: 1.88 Conformation dependent library (CDL) restraints added in 1.1 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: 0.95 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: 2.55 Time building geometry restraints manager: 2.21 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: 0.960 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.450 Find NCS groups from input model: 0.100 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:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.580 ------------------------------------------------------------------------------- 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 : 0.899 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 177 average time/residue: 1.1968 time to fit residues: 225.8256 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 : 0.851 ------------------------------------------------------------------------------- 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 = 0.119764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.106059 restraints weight = 10913.766| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.49 r_work: 0.3348 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 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 : 1.171 Fit side-chains REVERT: R 280 PHE cc_start: 0.8421 (t80) cc_final: 0.8204 (t80) REVERT: B 73 LYS cc_start: 0.8748 (mttp) cc_final: 0.8545 (mttm) REVERT: B 101 ASN cc_start: 0.8133 (t0) cc_final: 0.7694 (t0) outliers start: 19 outliers final: 9 residues processed: 173 average time/residue: 1.2123 time to fit residues: 222.5719 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 : 0.947 ------------------------------------------------------------------------------- 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: 0.6980 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 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 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 = 0.3652 r_free = 0.3652 target = 0.120648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.106985 restraints weight = 11133.726| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.48 r_work: 0.3357 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1241 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= 0.194 Angle : 0.547 5.834 11373 Z= 0.297 Chirality : 0.042 0.148 1329 Planarity : 0.004 0.047 1430 Dihedral : 4.090 19.058 1168 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.31 % Allowed : 11.79 % 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: 1.31 (0.26), residues: 1074 helix: 3.11 (0.28), residues: 355 sheet: 0.76 (0.30), residues: 279 loop : -1.02 (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 0.011 0.001 PHE C 151 TYR 0.014 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 187 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 1.004 Fit side-chains REVERT: R 280 PHE cc_start: 0.8414 (t80) cc_final: 0.8203 (t80) REVERT: C 304 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.8022 (mtm180) REVERT: C 312 ASP cc_start: 0.7680 (t0) cc_final: 0.7433 (t0) outliers start: 19 outliers final: 9 residues processed: 175 average time/residue: 1.2023 time to fit residues: 223.7331 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 : 0.927 ------------------------------------------------------------------------------- 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: 2.9990 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 90 optimal weight: 0.0980 chunk 64 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.120391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.106797 restraints weight = 11023.299| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.47 r_work: 0.3354 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8353 Z= 0.198 Angle : 0.544 5.926 11373 Z= 0.294 Chirality : 0.042 0.152 1329 Planarity : 0.004 0.047 1430 Dihedral : 4.082 19.048 1168 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.92 % Allowed : 12.64 % Favored : 84.45 % 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: 1.31 (0.26), residues: 1074 helix: 3.12 (0.28), residues: 355 sheet: 0.81 (0.30), residues: 279 loop : -1.07 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 190 HIS 0.005 0.001 HIS E 35 PHE 0.012 0.001 PHE C 234 TYR 0.014 0.001 TYR E 178 ARG 0.005 0.000 ARG B 132 *********************** 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 189 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.783 Fit side-chains REVERT: R 280 PHE cc_start: 0.8417 (t80) cc_final: 0.8208 (t80) REVERT: C 304 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8039 (mtm180) REVERT: C 312 ASP cc_start: 0.7695 (t0) cc_final: 0.7443 (t0) outliers start: 24 outliers final: 13 residues processed: 173 average time/residue: 1.1917 time to fit residues: 218.8785 Evaluate side-chains 184 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 37 ILE 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 243 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 107 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 E 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.120044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.106459 restraints weight = 10942.635| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.47 r_work: 0.3344 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1439 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= 0.218 Angle : 0.566 9.185 11373 Z= 0.306 Chirality : 0.043 0.211 1329 Planarity : 0.004 0.048 1430 Dihedral : 4.232 26.194 1168 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.28 % Allowed : 12.52 % Favored : 84.20 % 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: 1.28 (0.26), residues: 1074 helix: 3.10 (0.28), residues: 353 sheet: 0.86 (0.30), residues: 280 loop : -1.12 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 63 HIS 0.005 0.001 HIS E 35 PHE 0.012 0.001 PHE C 234 TYR 0.012 0.001 TYR E 178 ARG 0.004 0.000 ARG B 132 *********************** 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 196 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.889 Fit side-chains REVERT: R 280 PHE cc_start: 0.8415 (t80) cc_final: 0.8179 (t80) REVERT: C 304 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8037 (mtm180) REVERT: C 312 ASP cc_start: 0.7707 (t0) cc_final: 0.7456 (t0) outliers start: 27 outliers final: 14 residues processed: 180 average time/residue: 1.1402 time to fit residues: 218.2760 Evaluate side-chains 189 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 246 ILE 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 37 ILE 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 243 THR 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: 2.9990 chunk 62 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 C 88 ASN C 237 ASN E 159 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.118093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.104645 restraints weight = 10972.809| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.47 r_work: 0.3319 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8353 Z= 0.286 Angle : 0.622 8.208 11373 Z= 0.334 Chirality : 0.045 0.219 1329 Planarity : 0.004 0.051 1430 Dihedral : 4.457 28.724 1168 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.52 % Allowed : 13.00 % Favored : 83.48 % 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: 2.97 (0.28), residues: 353 sheet: 0.92 (0.31), residues: 274 loop : -1.17 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 63 HIS 0.007 0.001 HIS E 35 PHE 0.015 0.002 PHE C 151 TYR 0.015 0.002 TYR B 163 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 201 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.855 Fit side-chains REVERT: R 280 PHE cc_start: 0.8438 (t80) cc_final: 0.8206 (t80) REVERT: C 61 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8427 (ppp) REVERT: C 304 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8041 (mtm180) REVERT: C 312 ASP cc_start: 0.7733 (t0) cc_final: 0.7529 (t0) REVERT: E 128 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7420 (mtm) outliers start: 29 outliers final: 15 residues processed: 180 average time/residue: 1.1590 time to fit residues: 222.3173 Evaluate side-chains 188 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 21 LYS 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 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 189 SER 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 76 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 39 optimal weight: 0.0870 chunk 82 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.9162 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.118720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.105298 restraints weight = 11022.852| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.47 r_work: 0.3332 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8353 Z= 0.242 Angle : 0.588 7.175 11373 Z= 0.317 Chirality : 0.044 0.201 1329 Planarity : 0.004 0.051 1430 Dihedral : 4.367 27.378 1166 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.67 % Allowed : 15.43 % 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: 1.24 (0.26), residues: 1074 helix: 3.01 (0.28), residues: 353 sheet: 1.07 (0.31), residues: 265 loop : -1.20 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 63 HIS 0.005 0.001 HIS E 35 PHE 0.013 0.002 PHE C 151 TYR 0.014 0.002 TYR B 163 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 189 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.846 Fit side-chains REVERT: R 280 PHE cc_start: 0.8439 (t80) cc_final: 0.8199 (t80) REVERT: C 61 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8422 (ppp) REVERT: C 304 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8020 (mtm180) REVERT: C 312 ASP cc_start: 0.7737 (t0) cc_final: 0.7477 (t0) REVERT: E 128 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7282 (mtm) outliers start: 22 outliers final: 13 residues processed: 176 average time/residue: 1.1436 time to fit residues: 214.0945 Evaluate side-chains 184 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU 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 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 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 162 LEU Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 77 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 chunk 44 optimal weight: 0.0020 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN B 244 ASN C 75 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 = 0.3639 r_free = 0.3639 target = 0.119661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.106043 restraints weight = 11068.478| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.48 r_work: 0.3341 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8353 Z= 0.212 Angle : 0.562 6.639 11373 Z= 0.304 Chirality : 0.043 0.192 1329 Planarity : 0.004 0.049 1430 Dihedral : 4.261 26.112 1166 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.04 % Allowed : 15.31 % 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: 1.30 (0.26), residues: 1074 helix: 3.10 (0.28), residues: 353 sheet: 0.99 (0.30), residues: 271 loop : -1.16 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 63 HIS 0.005 0.001 HIS E 35 PHE 0.012 0.001 PHE C 151 TYR 0.014 0.001 TYR B 163 ARG 0.006 0.000 ARG B 132 *********************** 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 195 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.968 Fit side-chains REVERT: R 280 PHE cc_start: 0.8426 (t80) cc_final: 0.8191 (t80) REVERT: C 61 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8413 (ppp) REVERT: C 262 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8473 (tpt) REVERT: C 304 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8022 (mtm180) REVERT: C 312 ASP cc_start: 0.7739 (t0) cc_final: 0.7476 (t0) REVERT: E 93 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8547 (ttp) REVERT: E 128 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7234 (mtm) outliers start: 25 outliers final: 16 residues processed: 178 average time/residue: 1.1822 time to fit residues: 223.4542 Evaluate side-chains 192 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain B residue 25 GLU 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 61 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 189 SER 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 262 MET Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 33 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 E 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.119097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.105471 restraints weight = 11218.585| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.49 r_work: 0.3331 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8353 Z= 0.236 Angle : 0.588 7.346 11373 Z= 0.317 Chirality : 0.043 0.194 1329 Planarity : 0.004 0.052 1430 Dihedral : 4.335 26.881 1166 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.79 % Allowed : 15.67 % Favored : 81.53 % 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: 1.26 (0.26), residues: 1074 helix: 3.07 (0.28), residues: 353 sheet: 0.98 (0.30), residues: 272 loop : -1.19 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 63 HIS 0.006 0.001 HIS E 35 PHE 0.013 0.002 PHE C 151 TYR 0.014 0.002 TYR B 163 ARG 0.014 0.000 ARG B 132 *********************** 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 191 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.946 Fit side-chains REVERT: R 280 PHE cc_start: 0.8429 (t80) cc_final: 0.8183 (t80) REVERT: C 61 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8416 (ppp) REVERT: C 262 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8499 (tpt) REVERT: C 304 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8007 (mtm180) REVERT: C 312 ASP cc_start: 0.7735 (t0) cc_final: 0.7493 (t0) REVERT: E 93 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8513 (ttp) REVERT: E 128 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7275 (mtm) outliers start: 23 outliers final: 16 residues processed: 174 average time/residue: 1.1753 time to fit residues: 217.3528 Evaluate side-chains 189 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU 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 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 189 SER Chi-restraints excluded: chain C residue 220 GLN 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 262 MET Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 LEU 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 14 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 86 optimal weight: 0.0470 chunk 5 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 44 optimal weight: 0.0030 chunk 34 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 overall best weight: 0.4688 ------------------------------------------------------------------------------- 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 E 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.121779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.108112 restraints weight = 11032.060| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.47 r_work: 0.3373 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.002 0.027 8353 Z= 0.160 Angle : 0.524 7.307 11373 Z= 0.283 Chirality : 0.041 0.173 1329 Planarity : 0.004 0.056 1430 Dihedral : 4.062 23.350 1166 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.31 % Allowed : 16.28 % Favored : 81.41 % 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: 1.45 (0.26), residues: 1074 helix: 3.29 (0.28), residues: 353 sheet: 1.01 (0.31), residues: 273 loop : -1.08 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 63 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE R 81 TYR 0.013 0.001 TYR E 178 ARG 0.013 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 184 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.870 Fit side-chains REVERT: R 126 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7756 (mm-30) REVERT: R 280 PHE cc_start: 0.8402 (t80) cc_final: 0.8169 (t80) REVERT: C 262 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8461 (tpt) REVERT: C 304 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7999 (mtm180) REVERT: C 312 ASP cc_start: 0.7701 (t0) cc_final: 0.7477 (t0) REVERT: E 93 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8516 (ttp) REVERT: E 128 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7171 (mtm) outliers start: 19 outliers final: 12 residues processed: 171 average time/residue: 1.2214 time to fit residues: 221.4889 Evaluate side-chains 179 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU 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 220 GLN 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 262 MET Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 93 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.1980 chunk 80 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 27 optimal weight: 0.0870 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN C 54 HIS C 75 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 = 0.3678 r_free = 0.3678 target = 0.122486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.108707 restraints weight = 11200.966| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.49 r_work: 0.3383 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8353 Z= 0.153 Angle : 0.521 10.025 11373 Z= 0.279 Chirality : 0.041 0.167 1329 Planarity : 0.004 0.054 1430 Dihedral : 3.943 22.360 1166 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.67 % Allowed : 16.28 % Favored : 81.04 % 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: 1.54 (0.26), residues: 1074 helix: 3.38 (0.27), residues: 352 sheet: 1.01 (0.30), residues: 275 loop : -1.00 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 63 HIS 0.003 0.001 HIS E 35 PHE 0.009 0.001 PHE C 151 TYR 0.014 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: 7298.36 seconds wall clock time: 128 minutes 56.73 seconds (7736.73 seconds total)