Starting phenix.real_space_refine on Wed Sep 17 16:38:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9flz_50545/09_2025/9flz_50545.cif Found real_map, /net/cci-nas-00/data/ceres_data/9flz_50545/09_2025/9flz_50545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9flz_50545/09_2025/9flz_50545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9flz_50545/09_2025/9flz_50545.map" model { file = "/net/cci-nas-00/data/ceres_data/9flz_50545/09_2025/9flz_50545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9flz_50545/09_2025/9flz_50545.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 8 6.06 5 S 64 5.16 5 C 6269 2.51 5 N 1730 2.21 5 O 1837 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9908 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2470 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 315} Chain breaks: 1 Chain: "B" Number of atoms: 2479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2479 Classifications: {'peptide': 337} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 316} Chain breaks: 1 Chain: "C" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2467 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 315} Chain breaks: 1 Chain: "D" Number of atoms: 2478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2478 Classifications: {'peptide': 337} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 316} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 699 SG CYS A 96 40.813 39.723 47.668 1.00 23.47 S ATOM 719 SG CYS A 99 41.940 42.994 46.452 1.00 21.03 S ATOM 746 SG CYS A 102 41.902 42.378 50.169 1.00 19.43 S ATOM 806 SG CYS A 110 38.528 42.585 48.368 1.00 21.92 S ATOM 1124 SG CYS A 152 32.152 56.372 60.985 1.00 27.70 S ATOM 3169 SG CYS B 96 51.757 38.633 62.467 1.00 26.52 S ATOM 3189 SG CYS B 99 53.694 41.752 61.858 1.00 23.06 S ATOM 3216 SG CYS B 102 52.541 39.732 58.864 1.00 21.17 S ATOM 3276 SG CYS B 110 55.201 38.239 61.154 1.00 23.62 S ATOM 2765 SG CYS B 42 69.392 31.843 46.063 1.00 38.67 S ATOM 3594 SG CYS B 152 65.788 33.529 46.098 1.00 26.63 S ATOM 5632 SG CYS C 96 73.891 73.146 39.734 1.00 27.50 S ATOM 5652 SG CYS C 99 72.545 69.880 40.878 1.00 24.96 S ATOM 5679 SG CYS C 102 71.527 73.038 42.684 1.00 23.57 S ATOM 5739 SG CYS C 110 75.106 71.787 43.066 1.00 24.20 S ATOM 5228 SG CYS C 42 78.040 71.327 64.452 1.00 42.65 S ATOM 6057 SG CYS C 152 75.048 72.548 61.836 1.00 29.02 S ATOM 8106 SG CYS D 96 58.564 82.699 44.571 1.00 28.90 S ATOM 8126 SG CYS D 99 56.560 79.594 45.665 1.00 23.85 S ATOM 8153 SG CYS D 102 59.069 79.259 42.999 1.00 21.88 S ATOM 8213 SG CYS D 110 55.932 81.296 42.255 1.00 22.68 S ATOM 7702 SG CYS D 42 48.570 73.378 23.758 1.00 41.45 S ATOM 8531 SG CYS D 152 52.332 73.246 26.179 1.00 26.57 S Time building chain proxies: 2.60, per 1000 atoms: 0.26 Number of scatterers: 9908 At special positions: 0 Unit cell: (106.172, 104.5, 91.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 8 29.99 S 64 16.00 O 1837 8.00 N 1730 7.00 C 6269 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.97 Conformation dependent library (CDL) restraints added in 423.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 96 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 99 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 110 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" NE2 HIS A 65 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 152 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 96 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 99 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 110 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 102 " pdb=" ZN B1002 " pdb="ZN ZN B1002 " - pdb=" NE2 HIS B 65 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 42 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 152 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 96 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 99 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 102 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 110 " pdb=" ZN C1002 " pdb="ZN ZN C1002 " - pdb=" NE2 HIS C 65 " pdb="ZN ZN C1002 " - pdb=" SG CYS C 42 " pdb="ZN ZN C1002 " - pdb=" SG CYS C 152 " pdb=" ZN D1001 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 102 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 99 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 96 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 110 " pdb=" ZN D1002 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 152 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 42 " pdb="ZN ZN D1002 " - pdb=" NE2 HIS D 65 " Number of angles added : 24 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2330 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 17 sheets defined 34.7% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 42 through 51 Processing helix chain 'A' and resid 99 through 104 Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 152 through 163 Processing helix chain 'A' and resid 180 through 191 Processing helix chain 'A' and resid 201 through 212 removed outlier: 3.542A pdb=" N LEU A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 232 removed outlier: 3.577A pdb=" N ALA A 228 " --> pdb=" O ASP A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 276 through 284 Processing helix chain 'A' and resid 294 through 307 Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'A' and resid 321 through 329 Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.578A pdb=" N LEU B 46 " --> pdb=" O CYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 110 removed outlier: 3.507A pdb=" N CYS B 110 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 148 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 152 through 164 Processing helix chain 'B' and resid 178 through 191 Processing helix chain 'B' and resid 202 through 212 Processing helix chain 'B' and resid 224 through 233 removed outlier: 3.502A pdb=" N ALA B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 276 through 283 Processing helix chain 'B' and resid 294 through 307 Processing helix chain 'B' and resid 318 through 320 No H-bonds generated for 'chain 'B' and resid 318 through 320' Processing helix chain 'B' and resid 321 through 329 Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 99 through 104 Processing helix chain 'C' and resid 106 through 110 Processing helix chain 'C' and resid 143 through 148 Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 152 through 163 Processing helix chain 'C' and resid 178 through 191 Processing helix chain 'C' and resid 202 through 212 Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 276 through 283 Processing helix chain 'C' and resid 294 through 307 Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 321 through 332 Processing helix chain 'D' and resid 42 through 51 removed outlier: 3.500A pdb=" N LEU D 46 " --> pdb=" O CYS D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 104 Processing helix chain 'D' and resid 106 through 110 Processing helix chain 'D' and resid 152 through 163 Processing helix chain 'D' and resid 178 through 190 Processing helix chain 'D' and resid 202 through 212 Processing helix chain 'D' and resid 224 through 233 removed outlier: 3.676A pdb=" N ALA D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 256 Processing helix chain 'D' and resid 277 through 283 Processing helix chain 'D' and resid 294 through 307 Processing helix chain 'D' and resid 321 through 329 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 9 Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 130 removed outlier: 6.467A pdb=" N GLN A 33 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL A 68 " --> pdb=" O GLN A 37 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A 67 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 94 removed outlier: 6.342A pdb=" N LEU A 114 " --> pdb=" O TYR A 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 213 through 218 removed outlier: 6.828A pdb=" N VAL A 195 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP A 199 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP A 171 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N GLN A 238 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ALA D 237 " --> pdb=" O ALA D 258 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLY D 260 " --> pdb=" O ALA D 237 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N GLY D 239 " --> pdb=" O GLY D 260 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR D 262 " --> pdb=" O GLY D 239 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU D 241 " --> pdb=" O THR D 262 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA D 264 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP D 171 " --> pdb=" O ALA D 237 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL D 215 " --> pdb=" O VAL D 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 272 through 273 Processing sheet with id=AA6, first strand: chain 'A' and resid 314 through 317 removed outlier: 3.504A pdb=" N HIS A 315 " --> pdb=" O ARG A 337 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 7 through 9 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 removed outlier: 6.314A pdb=" N GLN B 33 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL B 68 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY B 67 " --> pdb=" O VAL B 89 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 215 through 218 removed outlier: 6.637A pdb=" N VAL B 195 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL B 217 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA B 197 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 198 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TRP B 171 " --> pdb=" O GLY B 239 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU B 241 " --> pdb=" O TRP B 171 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL B 173 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN B 238 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ALA B 264 " --> pdb=" O GLN B 238 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL B 240 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA C 237 " --> pdb=" O ALA C 258 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N GLY C 260 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLY C 239 " --> pdb=" O GLY C 260 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR C 262 " --> pdb=" O GLY C 239 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LEU C 241 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ALA C 264 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP C 171 " --> pdb=" O GLY C 239 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU C 241 " --> pdb=" O TRP C 171 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL C 173 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 275 Processing sheet with id=AB2, first strand: chain 'B' and resid 314 through 317 removed outlier: 3.618A pdb=" N VAL B 339 " --> pdb=" O HIS B 315 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 7 through 9 removed outlier: 3.647A pdb=" N THR C 18 " --> pdb=" O VAL C 9 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 127 through 130 removed outlier: 6.496A pdb=" N GLN C 33 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C 68 " --> pdb=" O GLN C 37 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY C 67 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 127 through 130 removed outlier: 4.428A pdb=" N MET C 338 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N HIS C 315 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASP C 341 " --> pdb=" O HIS C 315 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ALA C 317 " --> pdb=" O ASP C 341 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 7 through 9 Processing sheet with id=AB7, first strand: chain 'D' and resid 127 through 130 removed outlier: 5.956A pdb=" N ARG D 35 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N VAL D 71 " --> pdb=" O ARG D 35 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLN D 37 " --> pdb=" O GLY D 69 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLY D 69 " --> pdb=" O GLN D 37 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER D 39 " --> pdb=" O GLY D 67 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY D 67 " --> pdb=" O SER D 39 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY D 67 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 127 through 130 removed outlier: 3.617A pdb=" N VAL D 339 " --> pdb=" O HIS D 315 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1134 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: 1.76 Time building geometry restraints manager: 1.26 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: 3331 1.34 - 1.46: 1944 1.46 - 1.58: 4723 1.58 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 10102 Sorted by residual: bond pdb=" CA ALA C 219 " pdb=" C ALA C 219 " ideal model delta sigma weight residual 1.523 1.503 0.020 1.80e-02 3.09e+03 1.27e+00 bond pdb=" CA GLY C 267 " pdb=" C GLY C 267 " ideal model delta sigma weight residual 1.522 1.512 0.010 1.06e-02 8.90e+03 8.70e-01 bond pdb=" C ASN C 266 " pdb=" N GLY C 267 " ideal model delta sigma weight residual 1.336 1.327 0.009 1.01e-02 9.80e+03 8.30e-01 bond pdb=" CA PHE A 124 " pdb=" C PHE A 124 " ideal model delta sigma weight residual 1.531 1.521 0.010 1.12e-02 7.97e+03 7.48e-01 bond pdb=" C ASP A 224 " pdb=" O ASP A 224 " ideal model delta sigma weight residual 1.248 1.238 0.011 1.26e-02 6.30e+03 7.16e-01 ... (remaining 10097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 13072 1.17 - 2.34: 528 2.34 - 3.51: 97 3.51 - 4.68: 21 4.68 - 5.85: 8 Bond angle restraints: 13726 Sorted by residual: angle pdb=" N ILE C 291 " pdb=" CA ILE C 291 " pdb=" C ILE C 291 " ideal model delta sigma weight residual 109.46 105.13 4.33 1.38e+00 5.25e-01 9.84e+00 angle pdb=" C ARG C 247 " pdb=" N LYS C 248 " pdb=" CA LYS C 248 " ideal model delta sigma weight residual 121.54 127.14 -5.60 1.91e+00 2.74e-01 8.60e+00 angle pdb=" C VAL D 292 " pdb=" N GLY D 293 " pdb=" CA GLY D 293 " ideal model delta sigma weight residual 122.64 118.96 3.68 1.46e+00 4.69e-01 6.37e+00 angle pdb=" C ILE C 291 " pdb=" N VAL C 292 " pdb=" CA VAL C 292 " ideal model delta sigma weight residual 120.49 123.92 -3.43 1.38e+00 5.25e-01 6.19e+00 angle pdb=" N GLY D 123 " pdb=" CA GLY D 123 " pdb=" C GLY D 123 " ideal model delta sigma weight residual 114.66 117.72 -3.06 1.24e+00 6.50e-01 6.08e+00 ... (remaining 13721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 5503 17.84 - 35.67: 337 35.67 - 53.51: 65 53.51 - 71.34: 24 71.34 - 89.18: 19 Dihedral angle restraints: 5948 sinusoidal: 2256 harmonic: 3692 Sorted by residual: dihedral pdb=" CA ILE B 291 " pdb=" C ILE B 291 " pdb=" N VAL B 292 " pdb=" CA VAL B 292 " ideal model delta harmonic sigma weight residual 180.00 -156.36 -23.64 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA ILE D 291 " pdb=" C ILE D 291 " pdb=" N VAL D 292 " pdb=" CA VAL D 292 " ideal model delta harmonic sigma weight residual -180.00 -156.59 -23.41 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA THR A 313 " pdb=" C THR A 313 " pdb=" N VAL A 314 " pdb=" CA VAL A 314 " ideal model delta harmonic sigma weight residual -180.00 -161.50 -18.50 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 5945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 803 0.028 - 0.055: 420 0.055 - 0.083: 184 0.083 - 0.111: 110 0.111 - 0.139: 40 Chirality restraints: 1557 Sorted by residual: chirality pdb=" CA ILE C 62 " pdb=" N ILE C 62 " pdb=" C ILE C 62 " pdb=" CB ILE C 62 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA ILE B 62 " pdb=" N ILE B 62 " pdb=" C ILE B 62 " pdb=" CB ILE B 62 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE C 291 " pdb=" N ILE C 291 " pdb=" C ILE C 291 " pdb=" CB ILE C 291 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1554 not shown) Planarity restraints: 1803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 248 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C LYS C 248 " 0.037 2.00e-02 2.50e+03 pdb=" O LYS C 248 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA C 249 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 269 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO A 270 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 270 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 270 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 56 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO C 57 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 57 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 57 " -0.021 5.00e-02 4.00e+02 ... (remaining 1800 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1191 2.75 - 3.29: 9787 3.29 - 3.82: 17327 3.82 - 4.36: 21539 4.36 - 4.90: 35659 Nonbonded interactions: 85503 Sorted by model distance: nonbonded pdb=" OE1 GLN C 33 " pdb=" OG SER C 72 " model vdw 2.211 3.040 nonbonded pdb=" NZ LYS A 162 " pdb=" OD1 ASP A 297 " model vdw 2.269 3.120 nonbonded pdb=" O CYS B 110 " pdb=" NH1 ARG C 259 " model vdw 2.277 3.120 nonbonded pdb=" N ASP B 143 " pdb=" OD1 ASP B 143 " model vdw 2.279 3.120 nonbonded pdb=" O CYS C 152 " pdb=" OG1 THR C 156 " model vdw 2.284 3.040 ... (remaining 85498 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 1002) selection = (chain 'B' and (resid 5 through 330 or resid 336 through 1002)) selection = (chain 'C' and (resid 5 through 330 or resid 336 through 1002)) selection = (chain 'D' and (resid 5 through 330 or resid 336 through 1002)) } 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: 1.100 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.420 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10129 Z= 0.166 Angle : 0.581 6.130 13750 Z= 0.324 Chirality : 0.046 0.139 1557 Planarity : 0.004 0.041 1803 Dihedral : 13.821 89.180 3618 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.71 % Allowed : 7.80 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.21), residues: 1330 helix: -0.83 (0.22), residues: 455 sheet: -0.85 (0.34), residues: 204 loop : -1.59 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 259 TYR 0.010 0.002 TYR A 134 PHE 0.008 0.001 PHE A 273 TRP 0.006 0.001 TRP B 91 HIS 0.003 0.001 HIS C 182 Details of bonding type rmsd covalent geometry : bond 0.00359 (10102) covalent geometry : angle 0.57005 (13726) hydrogen bonds : bond 0.15910 ( 403) hydrogen bonds : angle 7.24290 ( 1134) metal coordination : bond 0.00620 ( 27) metal coordination : angle 2.71297 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.416 Fit side-chains REVERT: A 12 GLU cc_start: 0.7181 (pt0) cc_final: 0.6953 (pm20) REVERT: A 21 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6737 (tp30) REVERT: A 80 HIS cc_start: 0.6582 (t70) cc_final: 0.6297 (t-90) REVERT: A 329 MET cc_start: 0.6848 (OUTLIER) cc_final: 0.6349 (mmt) REVERT: A 342 MET cc_start: 0.6677 (ptp) cc_final: 0.6040 (ptp) REVERT: B 56 LYS cc_start: 0.8114 (mttp) cc_final: 0.7842 (mttt) REVERT: C 151 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7932 (mp) REVERT: C 200 ILE cc_start: 0.7328 (pt) cc_final: 0.7033 (mt) REVERT: D 6 LYS cc_start: 0.6546 (OUTLIER) cc_final: 0.6203 (mmmt) REVERT: D 26 GLU cc_start: 0.5985 (OUTLIER) cc_final: 0.5673 (tt0) REVERT: D 111 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6736 (mp0) REVERT: D 313 THR cc_start: 0.7591 (OUTLIER) cc_final: 0.7245 (m) REVERT: D 320 GLU cc_start: 0.7493 (mp0) cc_final: 0.7113 (mp0) REVERT: D 330 HIS cc_start: 0.6559 (m170) cc_final: 0.6333 (m170) outliers start: 38 outliers final: 16 residues processed: 212 average time/residue: 0.5527 time to fit residues: 126.2442 Evaluate side-chains 164 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 313 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.0670 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 232 GLN A 238 GLN A 315 HIS B 33 GLN B 266 ASN C 324 ASN D 232 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.130366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.113119 restraints weight = 11771.544| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.26 r_work: 0.3170 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10129 Z= 0.268 Angle : 0.690 9.280 13750 Z= 0.352 Chirality : 0.051 0.326 1557 Planarity : 0.005 0.037 1803 Dihedral : 7.339 59.210 1440 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.20 % Allowed : 12.49 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.22), residues: 1330 helix: -0.70 (0.23), residues: 464 sheet: -0.33 (0.37), residues: 176 loop : -1.61 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 259 TYR 0.015 0.003 TYR A 134 PHE 0.012 0.002 PHE D 70 TRP 0.014 0.002 TRP B 91 HIS 0.008 0.001 HIS C 182 Details of bonding type rmsd covalent geometry : bond 0.00622 (10102) covalent geometry : angle 0.67147 (13726) hydrogen bonds : bond 0.05038 ( 403) hydrogen bonds : angle 5.77944 ( 1134) metal coordination : bond 0.00829 ( 27) metal coordination : angle 3.90203 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 0.391 Fit side-chains REVERT: A 12 GLU cc_start: 0.7531 (pt0) cc_final: 0.7231 (pm20) REVERT: A 80 HIS cc_start: 0.6568 (t70) cc_final: 0.6208 (t-90) REVERT: A 329 MET cc_start: 0.6884 (OUTLIER) cc_final: 0.6331 (mmt) REVERT: A 342 MET cc_start: 0.7052 (ptp) cc_final: 0.6369 (ptp) REVERT: B 56 LYS cc_start: 0.8265 (mttp) cc_final: 0.8013 (mttt) REVERT: B 230 ARG cc_start: 0.7487 (mtm180) cc_final: 0.7246 (mtm110) REVERT: C 151 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8098 (mp) REVERT: D 26 GLU cc_start: 0.6136 (OUTLIER) cc_final: 0.5873 (tm-30) REVERT: D 111 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7032 (mp0) REVERT: D 313 THR cc_start: 0.7969 (t) cc_final: 0.7654 (m) outliers start: 43 outliers final: 25 residues processed: 179 average time/residue: 0.5028 time to fit residues: 97.6923 Evaluate side-chains 173 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 282 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 315 HIS C 324 ASN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.133058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.115763 restraints weight = 11713.178| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.26 r_work: 0.3213 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10129 Z= 0.138 Angle : 0.551 7.362 13750 Z= 0.280 Chirality : 0.046 0.284 1557 Planarity : 0.004 0.034 1803 Dihedral : 6.609 59.433 1436 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.51 % Allowed : 14.63 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.22), residues: 1330 helix: -0.34 (0.23), residues: 478 sheet: -0.51 (0.35), residues: 199 loop : -1.30 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 86 TYR 0.012 0.002 TYR C 158 PHE 0.008 0.001 PHE D 70 TRP 0.011 0.001 TRP B 91 HIS 0.006 0.001 HIS C 182 Details of bonding type rmsd covalent geometry : bond 0.00313 (10102) covalent geometry : angle 0.53542 (13726) hydrogen bonds : bond 0.03743 ( 403) hydrogen bonds : angle 5.20140 ( 1134) metal coordination : bond 0.00405 ( 27) metal coordination : angle 3.16282 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.370 Fit side-chains REVERT: A 12 GLU cc_start: 0.7537 (pt0) cc_final: 0.7231 (pm20) REVERT: A 80 HIS cc_start: 0.6451 (t70) cc_final: 0.6122 (t-90) REVERT: A 134 TYR cc_start: 0.8323 (m-80) cc_final: 0.8096 (m-80) REVERT: A 342 MET cc_start: 0.7090 (ptp) cc_final: 0.6429 (ptp) REVERT: B 56 LYS cc_start: 0.8265 (mttp) cc_final: 0.8019 (mttt) REVERT: C 151 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8040 (mp) REVERT: C 324 ASN cc_start: 0.6596 (m-40) cc_final: 0.6055 (m-40) REVERT: D 26 GLU cc_start: 0.6056 (OUTLIER) cc_final: 0.5777 (tt0) REVERT: D 111 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7132 (mp0) REVERT: D 191 MET cc_start: 0.7649 (mtt) cc_final: 0.7317 (mtt) REVERT: D 202 ASP cc_start: 0.7444 (t0) cc_final: 0.6962 (t0) REVERT: D 313 THR cc_start: 0.7963 (OUTLIER) cc_final: 0.7636 (m) outliers start: 36 outliers final: 15 residues processed: 180 average time/residue: 0.4648 time to fit residues: 91.2521 Evaluate side-chains 164 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 313 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 60 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 315 HIS D 232 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.131475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.114005 restraints weight = 11737.505| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.25 r_work: 0.3184 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10129 Z= 0.228 Angle : 0.634 8.310 13750 Z= 0.322 Chirality : 0.049 0.325 1557 Planarity : 0.005 0.037 1803 Dihedral : 6.424 59.657 1424 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.29 % Allowed : 15.22 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.22), residues: 1330 helix: -0.40 (0.23), residues: 470 sheet: -0.50 (0.35), residues: 194 loop : -1.37 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 259 TYR 0.013 0.002 TYR A 158 PHE 0.011 0.001 PHE D 70 TRP 0.013 0.002 TRP B 91 HIS 0.007 0.001 HIS C 182 Details of bonding type rmsd covalent geometry : bond 0.00529 (10102) covalent geometry : angle 0.61760 (13726) hydrogen bonds : bond 0.04394 ( 403) hydrogen bonds : angle 5.32856 ( 1134) metal coordination : bond 0.00690 ( 27) metal coordination : angle 3.52502 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 0.376 Fit side-chains REVERT: A 80 HIS cc_start: 0.6502 (t70) cc_final: 0.6155 (t-90) REVERT: A 342 MET cc_start: 0.7098 (ptp) cc_final: 0.6469 (ptp) REVERT: B 56 LYS cc_start: 0.8286 (mttp) cc_final: 0.8030 (mttt) REVERT: B 230 ARG cc_start: 0.7477 (mtm180) cc_final: 0.7224 (mtm110) REVERT: B 309 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7824 (mtpp) REVERT: C 111 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6501 (mp0) REVERT: C 151 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8050 (mp) REVERT: C 324 ASN cc_start: 0.6546 (m-40) cc_final: 0.5993 (m-40) REVERT: C 342 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6647 (mpt) REVERT: D 26 GLU cc_start: 0.6072 (OUTLIER) cc_final: 0.5818 (tt0) REVERT: D 111 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7177 (mp0) REVERT: D 230 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6911 (mtt180) REVERT: D 313 THR cc_start: 0.7985 (t) cc_final: 0.7649 (m) REVERT: D 342 MET cc_start: 0.7122 (OUTLIER) cc_final: 0.6128 (mtm) outliers start: 44 outliers final: 25 residues processed: 179 average time/residue: 0.4721 time to fit residues: 92.0327 Evaluate side-chains 172 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 342 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 126 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 315 HIS A 330 HIS D 232 GLN D 328 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.132261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.114835 restraints weight = 11618.515| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.25 r_work: 0.3200 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10129 Z= 0.176 Angle : 0.592 7.727 13750 Z= 0.299 Chirality : 0.047 0.289 1557 Planarity : 0.004 0.041 1803 Dihedral : 6.279 59.695 1424 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.71 % Allowed : 16.20 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.22), residues: 1330 helix: -0.32 (0.23), residues: 478 sheet: -0.41 (0.36), residues: 194 loop : -1.29 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 259 TYR 0.014 0.002 TYR C 158 PHE 0.009 0.001 PHE D 70 TRP 0.012 0.002 TRP B 91 HIS 0.007 0.001 HIS C 182 Details of bonding type rmsd covalent geometry : bond 0.00408 (10102) covalent geometry : angle 0.57655 (13726) hydrogen bonds : bond 0.03921 ( 403) hydrogen bonds : angle 5.14227 ( 1134) metal coordination : bond 0.00525 ( 27) metal coordination : angle 3.30953 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.389 Fit side-chains REVERT: A 12 GLU cc_start: 0.7605 (pt0) cc_final: 0.7303 (pm20) REVERT: A 21 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6777 (tp30) REVERT: A 80 HIS cc_start: 0.6482 (t70) cc_final: 0.6173 (t-90) REVERT: A 342 MET cc_start: 0.7110 (ptp) cc_final: 0.6477 (ptp) REVERT: B 56 LYS cc_start: 0.8281 (mttp) cc_final: 0.8025 (mttt) REVERT: B 309 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7813 (mtpp) REVERT: C 151 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8046 (mp) REVERT: C 324 ASN cc_start: 0.6565 (m-40) cc_final: 0.6009 (m-40) REVERT: C 342 MET cc_start: 0.7241 (OUTLIER) cc_final: 0.6693 (mpt) REVERT: D 26 GLU cc_start: 0.6072 (OUTLIER) cc_final: 0.5809 (tt0) REVERT: D 111 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7159 (mp0) REVERT: D 230 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6888 (mtt180) REVERT: D 313 THR cc_start: 0.7971 (OUTLIER) cc_final: 0.7630 (m) REVERT: D 342 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6136 (mtm) outliers start: 38 outliers final: 26 residues processed: 168 average time/residue: 0.4334 time to fit residues: 79.4781 Evaluate side-chains 167 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 342 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 4 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 100 optimal weight: 0.1980 chunk 123 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 315 HIS A 330 HIS D 232 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.134322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.116857 restraints weight = 11592.507| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.27 r_work: 0.3225 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10129 Z= 0.118 Angle : 0.537 7.044 13750 Z= 0.269 Chirality : 0.046 0.257 1557 Planarity : 0.004 0.041 1803 Dihedral : 5.856 59.194 1424 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.32 % Allowed : 17.17 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.23), residues: 1330 helix: 0.04 (0.23), residues: 479 sheet: -0.45 (0.35), residues: 219 loop : -1.08 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 35 TYR 0.008 0.001 TYR A 158 PHE 0.007 0.001 PHE D 70 TRP 0.009 0.001 TRP B 91 HIS 0.006 0.001 HIS C 182 Details of bonding type rmsd covalent geometry : bond 0.00269 (10102) covalent geometry : angle 0.52347 (13726) hydrogen bonds : bond 0.03310 ( 403) hydrogen bonds : angle 4.83972 ( 1134) metal coordination : bond 0.00326 ( 27) metal coordination : angle 2.90560 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.398 Fit side-chains REVERT: A 12 GLU cc_start: 0.7589 (pt0) cc_final: 0.7296 (pm20) REVERT: A 21 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6748 (tp30) REVERT: A 80 HIS cc_start: 0.6409 (t70) cc_final: 0.6146 (t-90) REVERT: A 342 MET cc_start: 0.7058 (ptp) cc_final: 0.6437 (ptp) REVERT: B 56 LYS cc_start: 0.8241 (mttp) cc_final: 0.7997 (mttt) REVERT: C 151 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7881 (mp) REVERT: C 324 ASN cc_start: 0.6596 (m-40) cc_final: 0.6039 (m110) REVERT: D 26 GLU cc_start: 0.6167 (OUTLIER) cc_final: 0.5810 (tt0) REVERT: D 83 GLU cc_start: 0.6599 (mt-10) cc_final: 0.6392 (mt-10) REVERT: D 111 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7143 (mp0) REVERT: D 202 ASP cc_start: 0.7476 (t0) cc_final: 0.7174 (t0) REVERT: D 230 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6895 (mtt180) REVERT: D 313 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7585 (m) REVERT: D 320 GLU cc_start: 0.7541 (mp0) cc_final: 0.7211 (mp0) REVERT: D 342 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6230 (mtm) outliers start: 34 outliers final: 17 residues processed: 183 average time/residue: 0.4740 time to fit residues: 94.2610 Evaluate side-chains 164 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 342 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 6 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 chunk 1 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 315 HIS ** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.132002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.114538 restraints weight = 11552.806| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.26 r_work: 0.3192 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10129 Z= 0.196 Angle : 0.603 7.635 13750 Z= 0.304 Chirality : 0.048 0.243 1557 Planarity : 0.004 0.037 1803 Dihedral : 5.993 59.449 1421 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.00 % Allowed : 17.56 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.22), residues: 1330 helix: -0.14 (0.23), residues: 479 sheet: -0.47 (0.35), residues: 213 loop : -1.17 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 100 TYR 0.012 0.002 TYR C 158 PHE 0.010 0.001 PHE D 70 TRP 0.010 0.002 TRP B 91 HIS 0.007 0.001 HIS C 182 Details of bonding type rmsd covalent geometry : bond 0.00453 (10102) covalent geometry : angle 0.58789 (13726) hydrogen bonds : bond 0.03978 ( 403) hydrogen bonds : angle 5.06645 ( 1134) metal coordination : bond 0.00579 ( 27) metal coordination : angle 3.22776 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 0.371 Fit side-chains REVERT: A 12 GLU cc_start: 0.7579 (pt0) cc_final: 0.7275 (pm20) REVERT: A 21 GLU cc_start: 0.7077 (mm-30) cc_final: 0.6756 (tp30) REVERT: A 80 HIS cc_start: 0.6454 (t70) cc_final: 0.6139 (t-90) REVERT: A 342 MET cc_start: 0.7108 (ptp) cc_final: 0.6496 (ptp) REVERT: B 56 LYS cc_start: 0.8262 (mttp) cc_final: 0.8013 (mttt) REVERT: B 309 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7842 (mtpp) REVERT: C 151 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8028 (mp) REVERT: C 324 ASN cc_start: 0.6560 (m-40) cc_final: 0.6010 (m-40) REVERT: D 26 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5905 (tt0) REVERT: D 111 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7164 (mp0) REVERT: D 230 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6908 (mtt180) REVERT: D 313 THR cc_start: 0.7980 (t) cc_final: 0.7644 (m) REVERT: D 342 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.6173 (mtm) outliers start: 41 outliers final: 25 residues processed: 172 average time/residue: 0.4720 time to fit residues: 88.2284 Evaluate side-chains 169 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 342 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 15 optimal weight: 0.7980 chunk 35 optimal weight: 0.0060 chunk 20 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 315 HIS A 330 HIS ** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.133773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.116438 restraints weight = 11596.313| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.25 r_work: 0.3221 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 : 0.003 0.035 10129 Z= 0.133 Angle : 0.555 7.115 13750 Z= 0.278 Chirality : 0.047 0.199 1557 Planarity : 0.004 0.038 1803 Dihedral : 5.750 58.746 1421 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.41 % Allowed : 18.05 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.22), residues: 1330 helix: 0.07 (0.23), residues: 479 sheet: -0.35 (0.36), residues: 203 loop : -1.05 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 100 TYR 0.011 0.002 TYR C 158 PHE 0.007 0.001 PHE D 70 TRP 0.009 0.001 TRP C 91 HIS 0.006 0.001 HIS C 182 Details of bonding type rmsd covalent geometry : bond 0.00305 (10102) covalent geometry : angle 0.54098 (13726) hydrogen bonds : bond 0.03434 ( 403) hydrogen bonds : angle 4.87583 ( 1134) metal coordination : bond 0.00379 ( 27) metal coordination : angle 2.97685 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.313 Fit side-chains REVERT: A 12 GLU cc_start: 0.7584 (pt0) cc_final: 0.7278 (pm20) REVERT: A 21 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6752 (tp30) REVERT: A 80 HIS cc_start: 0.6389 (t70) cc_final: 0.6096 (t-90) REVERT: A 342 MET cc_start: 0.7097 (ptp) cc_final: 0.6475 (ptp) REVERT: B 56 LYS cc_start: 0.8254 (mttp) cc_final: 0.8014 (mttt) REVERT: B 309 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7796 (mtpp) REVERT: C 151 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7891 (mp) REVERT: D 26 GLU cc_start: 0.6170 (OUTLIER) cc_final: 0.5839 (tt0) REVERT: D 111 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7153 (mp0) REVERT: D 230 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6894 (mtt180) REVERT: D 313 THR cc_start: 0.7919 (OUTLIER) cc_final: 0.7545 (m) REVERT: D 342 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6194 (mtm) outliers start: 35 outliers final: 19 residues processed: 172 average time/residue: 0.5086 time to fit residues: 94.6732 Evaluate side-chains 165 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 342 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 130 optimal weight: 4.9990 chunk 71 optimal weight: 0.0170 chunk 100 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS A 330 HIS B 43 HIS ** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.133822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.116557 restraints weight = 11584.829| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.25 r_work: 0.3222 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10129 Z= 0.136 Angle : 0.556 7.141 13750 Z= 0.278 Chirality : 0.046 0.193 1557 Planarity : 0.004 0.039 1803 Dihedral : 5.630 57.732 1417 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.12 % Allowed : 18.73 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.23), residues: 1330 helix: 0.15 (0.24), residues: 478 sheet: -0.43 (0.35), residues: 217 loop : -1.02 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 35 TYR 0.016 0.002 TYR C 158 PHE 0.008 0.001 PHE D 70 TRP 0.008 0.001 TRP C 91 HIS 0.006 0.001 HIS C 182 Details of bonding type rmsd covalent geometry : bond 0.00313 (10102) covalent geometry : angle 0.54310 (13726) hydrogen bonds : bond 0.03469 ( 403) hydrogen bonds : angle 4.85228 ( 1134) metal coordination : bond 0.00377 ( 27) metal coordination : angle 2.92070 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.332 Fit side-chains REVERT: A 12 GLU cc_start: 0.7593 (pt0) cc_final: 0.7283 (pm20) REVERT: A 21 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6714 (tp30) REVERT: A 80 HIS cc_start: 0.6351 (t70) cc_final: 0.6051 (t-90) REVERT: A 328 GLN cc_start: 0.5557 (tm-30) cc_final: 0.5110 (tm-30) REVERT: A 342 MET cc_start: 0.7113 (ptp) cc_final: 0.6491 (ptp) REVERT: B 56 LYS cc_start: 0.8254 (mttp) cc_final: 0.8017 (mttt) REVERT: B 222 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6609 (mm-30) REVERT: B 309 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7804 (mtpp) REVERT: C 151 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7939 (mp) REVERT: C 320 GLU cc_start: 0.7662 (mp0) cc_final: 0.7428 (mp0) REVERT: D 26 GLU cc_start: 0.6157 (OUTLIER) cc_final: 0.5820 (tm-30) REVERT: D 111 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7157 (mp0) REVERT: D 230 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6897 (mtt180) REVERT: D 313 THR cc_start: 0.7950 (OUTLIER) cc_final: 0.7591 (m) REVERT: D 342 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6189 (mtm) outliers start: 32 outliers final: 20 residues processed: 171 average time/residue: 0.4840 time to fit residues: 89.9658 Evaluate side-chains 169 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 342 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 64 optimal weight: 0.2980 chunk 128 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 121 optimal weight: 0.0980 chunk 39 optimal weight: 0.0000 chunk 131 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 overall best weight: 0.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN A 315 HIS B 43 HIS B 323 ASN D 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.137330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.120029 restraints weight = 11509.886| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.28 r_work: 0.3268 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10129 Z= 0.094 Angle : 0.518 6.778 13750 Z= 0.257 Chirality : 0.045 0.201 1557 Planarity : 0.004 0.044 1803 Dihedral : 5.196 58.772 1415 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.85 % Allowed : 20.10 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.23), residues: 1330 helix: 0.43 (0.24), residues: 478 sheet: -0.31 (0.35), residues: 217 loop : -0.92 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 35 TYR 0.011 0.001 TYR D 93 PHE 0.006 0.001 PHE A 273 TRP 0.008 0.001 TRP C 91 HIS 0.006 0.001 HIS C 182 Details of bonding type rmsd covalent geometry : bond 0.00212 (10102) covalent geometry : angle 0.50765 (13726) hydrogen bonds : bond 0.02915 ( 403) hydrogen bonds : angle 4.63293 ( 1134) metal coordination : bond 0.00251 ( 27) metal coordination : angle 2.48874 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.393 Fit side-chains REVERT: A 12 GLU cc_start: 0.7538 (pt0) cc_final: 0.7233 (pm20) REVERT: A 23 PRO cc_start: 0.7274 (Cg_exo) cc_final: 0.7045 (Cg_endo) REVERT: A 80 HIS cc_start: 0.6331 (t70) cc_final: 0.6089 (t-90) REVERT: A 328 GLN cc_start: 0.5593 (tm-30) cc_final: 0.5139 (tm-30) REVERT: A 342 MET cc_start: 0.7049 (ptp) cc_final: 0.6408 (ptp) REVERT: B 56 LYS cc_start: 0.8200 (mttp) cc_final: 0.7923 (mttp) REVERT: B 309 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7793 (mtpp) REVERT: D 11 ARG cc_start: 0.6688 (mmt90) cc_final: 0.6347 (mmm-85) REVERT: D 26 GLU cc_start: 0.5956 (OUTLIER) cc_final: 0.5684 (tm-30) REVERT: D 111 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7050 (mp0) REVERT: D 202 ASP cc_start: 0.7331 (t0) cc_final: 0.7011 (t0) REVERT: D 230 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6848 (mtt180) REVERT: D 313 THR cc_start: 0.7886 (OUTLIER) cc_final: 0.7510 (m) outliers start: 19 outliers final: 12 residues processed: 178 average time/residue: 0.5043 time to fit residues: 97.2140 Evaluate side-chains 166 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 313 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 95 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS B 43 HIS ** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN D 232 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.135345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.117867 restraints weight = 11581.987| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.28 r_work: 0.3236 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10129 Z= 0.124 Angle : 0.539 7.073 13750 Z= 0.268 Chirality : 0.046 0.186 1557 Planarity : 0.004 0.048 1803 Dihedral : 5.229 57.743 1413 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.85 % Allowed : 20.39 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.23), residues: 1330 helix: 0.38 (0.24), residues: 478 sheet: -0.23 (0.35), residues: 216 loop : -0.92 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 35 TYR 0.015 0.002 TYR A 158 PHE 0.007 0.001 PHE C 61 TRP 0.007 0.001 TRP B 91 HIS 0.006 0.001 HIS C 182 Details of bonding type rmsd covalent geometry : bond 0.00284 (10102) covalent geometry : angle 0.52785 (13726) hydrogen bonds : bond 0.03273 ( 403) hydrogen bonds : angle 4.70957 ( 1134) metal coordination : bond 0.00329 ( 27) metal coordination : angle 2.60549 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2991.11 seconds wall clock time: 51 minutes 45.42 seconds (3105.42 seconds total)