Starting phenix.real_space_refine on Sun Jul 27 22:55:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9flz_50545/07_2025/9flz_50545.cif Found real_map, /net/cci-nas-00/data/ceres_data/9flz_50545/07_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_50545/07_2025/9flz_50545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9flz_50545/07_2025/9flz_50545.map" model { file = "/net/cci-nas-00/data/ceres_data/9flz_50545/07_2025/9flz_50545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9flz_50545/07_2025/9flz_50545.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.48, per 1000 atoms: 0.65 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: 2.64 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.36 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: 3.13 Time building geometry restraints manager: 3.00 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 343 or resid 1001 through 1002)) selection = (chain 'B' and (resid 5 through 330 or resid 336 through 343 or resid 1001 throu \ gh 1002)) selection = (chain 'C' and (resid 5 through 330 or resid 336 through 343 or resid 1001 throu \ gh 1002)) selection = (chain 'D' and (resid 5 through 330 or resid 336 through 343 or resid 1001 throu \ gh 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.210 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.940 ------------------------------------------------------------------------------- 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 : 10.76 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (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 TRP 0.006 0.001 TRP B 91 HIS 0.003 0.001 HIS C 182 PHE 0.008 0.001 PHE A 273 TYR 0.010 0.002 TYR A 134 ARG 0.004 0.001 ARG A 259 Details of bonding type rmsd hydrogen bonds : bond 0.15910 ( 403) hydrogen bonds : angle 7.24290 ( 1134) metal coordination : bond 0.00620 ( 27) metal coordination : angle 2.71297 ( 24) covalent geometry : bond 0.00359 (10102) covalent geometry : angle 0.57005 (13726) *********************** 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 : 1.073 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: 1.1265 time to fit residues: 257.3634 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 : 1.226 ------------------------------------------------------------------------------- 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 111 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 0.0670 chunk 119 optimal weight: 0.9990 overall best weight: 1.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 238 GLN A 315 HIS B 266 ASN C 324 ASN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.132099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.114477 restraints weight = 11554.601| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.30 r_work: 0.3194 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10129 Z= 0.180 Angle : 0.602 7.966 13750 Z= 0.307 Chirality : 0.048 0.346 1557 Planarity : 0.004 0.035 1803 Dihedral : 6.938 59.675 1440 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.61 % Allowed : 12.68 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.22), residues: 1330 helix: -0.52 (0.23), residues: 478 sheet: -0.35 (0.36), residues: 187 loop : -1.38 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 91 HIS 0.008 0.001 HIS C 182 PHE 0.008 0.001 PHE D 70 TYR 0.012 0.002 TYR C 158 ARG 0.004 0.001 ARG B 288 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 403) hydrogen bonds : angle 5.54181 ( 1134) metal coordination : bond 0.00513 ( 27) metal coordination : angle 3.49391 ( 24) covalent geometry : bond 0.00410 (10102) covalent geometry : angle 0.58425 (13726) *********************** 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 196 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 1.080 Fit side-chains REVERT: A 12 GLU cc_start: 0.7564 (pt0) cc_final: 0.7240 (pm20) REVERT: A 80 HIS cc_start: 0.6540 (t70) cc_final: 0.6207 (t-90) REVERT: A 342 MET cc_start: 0.7047 (ptp) cc_final: 0.6325 (ptp) REVERT: B 56 LYS cc_start: 0.8253 (mttp) cc_final: 0.8009 (mttt) REVERT: B 230 ARG cc_start: 0.7405 (mtm180) cc_final: 0.7181 (mtm110) REVERT: C 151 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8090 (mp) REVERT: D 26 GLU cc_start: 0.6131 (OUTLIER) cc_final: 0.5857 (tt0) REVERT: D 111 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7182 (mp0) REVERT: D 313 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7655 (m) outliers start: 37 outliers final: 22 residues processed: 184 average time/residue: 1.1317 time to fit residues: 226.0448 Evaluate side-chains 174 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 A residue 341 ASP Chi-restraints excluded: chain B residue 85 ASP 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 313 THR 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 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 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 282 LEU Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 334 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 30 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 141 ASN A 232 GLN A 315 HIS B 33 GLN C 324 ASN D 232 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.132313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.115119 restraints weight = 11593.133| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.24 r_work: 0.3197 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10129 Z= 0.205 Angle : 0.611 8.171 13750 Z= 0.310 Chirality : 0.048 0.274 1557 Planarity : 0.004 0.035 1803 Dihedral : 6.533 59.477 1430 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.80 % Allowed : 14.05 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.22), residues: 1330 helix: -0.49 (0.23), residues: 478 sheet: -0.48 (0.35), residues: 194 loop : -1.37 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 91 HIS 0.008 0.001 HIS C 182 PHE 0.010 0.001 PHE D 70 TYR 0.014 0.002 TYR C 158 ARG 0.004 0.001 ARG A 259 Details of bonding type rmsd hydrogen bonds : bond 0.04337 ( 403) hydrogen bonds : angle 5.37399 ( 1134) metal coordination : bond 0.00631 ( 27) metal coordination : angle 3.46439 ( 24) covalent geometry : bond 0.00474 (10102) covalent geometry : angle 0.59380 (13726) *********************** 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 196 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 157 time to evaluate : 1.184 Fit side-chains REVERT: A 12 GLU cc_start: 0.7588 (pt0) cc_final: 0.7280 (pm20) REVERT: A 80 HIS cc_start: 0.6483 (t70) cc_final: 0.6149 (t-90) REVERT: A 342 MET cc_start: 0.7120 (ptp) cc_final: 0.6456 (ptp) REVERT: B 56 LYS cc_start: 0.8283 (mttp) cc_final: 0.8028 (mttt) REVERT: B 230 ARG cc_start: 0.7458 (mtm180) cc_final: 0.7207 (mtm110) REVERT: C 151 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8038 (mp) REVERT: C 324 ASN cc_start: 0.6576 (m-40) cc_final: 0.6026 (m-40) REVERT: D 26 GLU cc_start: 0.6087 (OUTLIER) cc_final: 0.5815 (tt0) REVERT: D 111 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7131 (mp0) REVERT: D 313 THR cc_start: 0.7974 (t) cc_final: 0.7647 (m) outliers start: 39 outliers final: 25 residues processed: 179 average time/residue: 1.1373 time to fit residues: 220.6942 Evaluate side-chains 169 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 B residue 85 ASP 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 40 optimal weight: 0.0670 chunk 46 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 89 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 chunk 87 optimal weight: 0.0370 overall best weight: 0.3596 ------------------------------------------------------------------------------- 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 A 330 HIS D 33 GLN D 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.136217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.119442 restraints weight = 11430.854| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.21 r_work: 0.3257 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10129 Z= 0.095 Angle : 0.513 8.993 13750 Z= 0.256 Chirality : 0.045 0.351 1557 Planarity : 0.004 0.036 1803 Dihedral : 5.752 58.043 1428 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.44 % Allowed : 16.20 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.23), residues: 1330 helix: 0.11 (0.24), residues: 478 sheet: -0.38 (0.36), residues: 204 loop : -1.08 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 91 HIS 0.005 0.001 HIS C 182 PHE 0.006 0.001 PHE D 70 TYR 0.009 0.001 TYR D 93 ARG 0.002 0.000 ARG C 35 Details of bonding type rmsd hydrogen bonds : bond 0.03067 ( 403) hydrogen bonds : angle 4.79093 ( 1134) metal coordination : bond 0.00237 ( 27) metal coordination : angle 2.71086 ( 24) covalent geometry : bond 0.00208 (10102) covalent geometry : angle 0.50070 (13726) *********************** 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 189 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 1.121 Fit side-chains REVERT: A 12 GLU cc_start: 0.7576 (pt0) cc_final: 0.7294 (pm20) REVERT: A 80 HIS cc_start: 0.6414 (t70) cc_final: 0.6133 (t-90) REVERT: A 342 MET cc_start: 0.7073 (ptp) cc_final: 0.6426 (ptp) REVERT: B 56 LYS cc_start: 0.8211 (mttp) cc_final: 0.7976 (mttt) REVERT: C 151 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7877 (mp) REVERT: C 291 ILE cc_start: 0.6755 (OUTLIER) cc_final: 0.6314 (pp) REVERT: C 324 ASN cc_start: 0.6627 (m-40) cc_final: 0.6086 (m-40) REVERT: D 26 GLU cc_start: 0.6129 (OUTLIER) cc_final: 0.5792 (tt0) REVERT: D 83 GLU cc_start: 0.6545 (mt-10) cc_final: 0.6335 (mt-10) REVERT: D 111 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7116 (mp0) REVERT: D 202 ASP cc_start: 0.7390 (t0) cc_final: 0.6945 (t0) REVERT: D 230 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6884 (mtt180) REVERT: D 313 THR cc_start: 0.7890 (OUTLIER) cc_final: 0.7528 (m) REVERT: D 320 GLU cc_start: 0.7468 (mp0) cc_final: 0.7127 (mp0) outliers start: 25 outliers final: 9 residues processed: 181 average time/residue: 1.0971 time to fit residues: 215.1732 Evaluate side-chains 159 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 313 THR 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 291 ILE 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 230 ARG Chi-restraints excluded: chain D residue 313 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 1 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS ** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.134169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.116709 restraints weight = 11340.830| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.25 r_work: 0.3215 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10129 Z= 0.149 Angle : 0.557 8.608 13750 Z= 0.279 Chirality : 0.047 0.286 1557 Planarity : 0.004 0.043 1803 Dihedral : 5.552 56.509 1418 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.93 % Allowed : 16.88 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.23), residues: 1330 helix: 0.10 (0.23), residues: 478 sheet: -0.45 (0.35), residues: 217 loop : -1.05 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 91 HIS 0.006 0.001 HIS C 182 PHE 0.008 0.001 PHE D 70 TYR 0.009 0.002 TYR A 134 ARG 0.005 0.000 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 403) hydrogen bonds : angle 4.86404 ( 1134) metal coordination : bond 0.00408 ( 27) metal coordination : angle 2.91411 ( 24) covalent geometry : bond 0.00345 (10102) covalent geometry : angle 0.54354 (13726) *********************** 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 182 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 1.058 Fit side-chains REVERT: A 12 GLU cc_start: 0.7591 (pt0) cc_final: 0.7293 (pm20) REVERT: A 21 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6862 (tp30) REVERT: A 80 HIS cc_start: 0.6386 (t70) cc_final: 0.6090 (t-90) REVERT: A 342 MET cc_start: 0.7078 (ptp) cc_final: 0.6438 (ptp) REVERT: B 56 LYS cc_start: 0.8244 (mttp) cc_final: 0.8008 (mttt) REVERT: B 309 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7777 (mtpp) REVERT: C 151 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8019 (mp) REVERT: C 324 ASN cc_start: 0.6573 (m-40) cc_final: 0.6067 (m-40) REVERT: D 26 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.5846 (tt0) REVERT: D 111 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7160 (mp0) REVERT: D 230 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6900 (mtt180) REVERT: D 313 THR cc_start: 0.7891 (t) cc_final: 0.7539 (m) outliers start: 30 outliers final: 15 residues processed: 173 average time/residue: 1.0485 time to fit residues: 197.7711 Evaluate side-chains 165 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 1.615 ------------------------------------------------------------------------------- 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 242 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 216 THR 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 151 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 242 VAL 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 94 THR Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 282 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 10 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** 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 = 0.3544 r_free = 0.3544 target = 0.133840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.116409 restraints weight = 11496.298| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.27 r_work: 0.3218 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10129 Z= 0.140 Angle : 0.550 7.292 13750 Z= 0.275 Chirality : 0.047 0.262 1557 Planarity : 0.004 0.043 1803 Dihedral : 5.534 56.113 1418 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.73 % Allowed : 17.95 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.23), residues: 1330 helix: 0.16 (0.23), residues: 479 sheet: -0.39 (0.35), residues: 215 loop : -1.01 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 91 HIS 0.006 0.001 HIS C 182 PHE 0.008 0.001 PHE D 70 TYR 0.020 0.002 TYR B 127 ARG 0.004 0.000 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 403) hydrogen bonds : angle 4.83433 ( 1134) metal coordination : bond 0.00384 ( 27) metal coordination : angle 2.92350 ( 24) covalent geometry : bond 0.00323 (10102) covalent geometry : angle 0.53683 (13726) *********************** 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 181 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 1.191 Fit side-chains REVERT: A 12 GLU cc_start: 0.7621 (pt0) cc_final: 0.7305 (pm20) REVERT: A 80 HIS cc_start: 0.6367 (t70) cc_final: 0.6077 (t-90) REVERT: A 342 MET cc_start: 0.7079 (ptp) cc_final: 0.6430 (ptp) REVERT: B 56 LYS cc_start: 0.8235 (mttp) cc_final: 0.7992 (mttt) REVERT: C 151 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7946 (mp) REVERT: D 26 GLU cc_start: 0.6208 (OUTLIER) cc_final: 0.5847 (tm-30) REVERT: D 111 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7153 (mp0) REVERT: D 230 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6912 (mtt180) REVERT: D 313 THR cc_start: 0.7961 (OUTLIER) cc_final: 0.7599 (m) REVERT: D 342 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6236 (mtm) outliers start: 28 outliers final: 16 residues processed: 172 average time/residue: 1.0743 time to fit residues: 200.6567 Evaluate side-chains 167 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 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 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 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 94 THR Chi-restraints excluded: chain D residue 230 ARG 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 22 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 73 optimal weight: 0.2980 chunk 50 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS ** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.134886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.117614 restraints weight = 11705.428| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.26 r_work: 0.3235 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1805 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= 0.112 Angle : 0.522 6.688 13750 Z= 0.259 Chirality : 0.046 0.232 1557 Planarity : 0.004 0.041 1803 Dihedral : 5.364 56.485 1418 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.93 % Allowed : 17.85 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.23), residues: 1330 helix: 0.35 (0.24), residues: 478 sheet: -0.37 (0.34), residues: 227 loop : -0.96 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 91 HIS 0.006 0.001 HIS C 182 PHE 0.007 0.001 PHE D 70 TYR 0.010 0.002 TYR A 158 ARG 0.003 0.000 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.03184 ( 403) hydrogen bonds : angle 4.69020 ( 1134) metal coordination : bond 0.00296 ( 27) metal coordination : angle 2.70147 ( 24) covalent geometry : bond 0.00255 (10102) covalent geometry : angle 0.50964 (13726) *********************** 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: 30 poor density : 155 time to evaluate : 1.134 Fit side-chains REVERT: A 12 GLU cc_start: 0.7598 (pt0) cc_final: 0.7286 (pm20) REVERT: A 80 HIS cc_start: 0.6410 (t70) cc_final: 0.6129 (t-90) REVERT: A 342 MET cc_start: 0.7068 (ptp) cc_final: 0.6420 (ptp) REVERT: B 56 LYS cc_start: 0.8215 (mttp) cc_final: 0.7986 (mttt) REVERT: B 309 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7769 (mtpp) REVERT: C 151 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7915 (mp) REVERT: D 26 GLU cc_start: 0.6052 (OUTLIER) cc_final: 0.5776 (tm-30) REVERT: D 111 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7160 (mp0) REVERT: D 230 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6893 (mtt180) REVERT: D 313 THR cc_start: 0.7924 (OUTLIER) cc_final: 0.7551 (m) outliers start: 30 outliers final: 16 residues processed: 174 average time/residue: 1.0158 time to fit residues: 192.4855 Evaluate side-chains 167 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 242 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 129 VAL 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 151 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 292 VAL 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 230 ARG Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 313 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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** ** C 43 HIS ** 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 = 0.3540 r_free = 0.3540 target = 0.133649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.116184 restraints weight = 11617.006| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.28 r_work: 0.3210 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1716 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= 0.156 Angle : 0.564 6.947 13750 Z= 0.281 Chirality : 0.047 0.199 1557 Planarity : 0.004 0.039 1803 Dihedral : 5.451 55.753 1414 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.22 % Allowed : 18.05 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.23), residues: 1330 helix: 0.21 (0.23), residues: 478 sheet: -0.31 (0.34), residues: 211 loop : -1.00 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 91 HIS 0.006 0.001 HIS C 43 PHE 0.009 0.001 PHE D 70 TYR 0.021 0.002 TYR A 158 ARG 0.003 0.000 ARG A 259 Details of bonding type rmsd hydrogen bonds : bond 0.03608 ( 403) hydrogen bonds : angle 4.84399 ( 1134) metal coordination : bond 0.00435 ( 27) metal coordination : angle 2.95878 ( 24) covalent geometry : bond 0.00361 (10102) covalent geometry : angle 0.55033 (13726) *********************** 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: 33 poor density : 150 time to evaluate : 1.063 Fit side-chains REVERT: A 12 GLU cc_start: 0.7596 (pt0) cc_final: 0.7292 (pm20) REVERT: A 80 HIS cc_start: 0.6316 (t70) cc_final: 0.5981 (t-90) REVERT: A 342 MET cc_start: 0.7101 (ptp) cc_final: 0.6457 (ptp) REVERT: B 56 LYS cc_start: 0.8266 (mttp) cc_final: 0.8032 (mttt) REVERT: B 309 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7783 (mtpp) REVERT: C 151 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7957 (mp) REVERT: D 26 GLU cc_start: 0.6104 (OUTLIER) cc_final: 0.5794 (tm-30) REVERT: D 111 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7147 (mp0) REVERT: D 230 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6935 (mtt180) REVERT: D 313 THR cc_start: 0.7909 (OUTLIER) cc_final: 0.7495 (m) REVERT: D 342 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6228 (mtm) outliers start: 33 outliers final: 16 residues processed: 169 average time/residue: 1.0321 time to fit residues: 190.2057 Evaluate side-chains 165 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 216 THR 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 151 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 282 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 22 optimal weight: 0.0470 chunk 42 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS ** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 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 = 0.3555 r_free = 0.3555 target = 0.134876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.117387 restraints weight = 11437.842| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.26 r_work: 0.3223 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1773 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= 0.139 Angle : 0.551 6.904 13750 Z= 0.275 Chirality : 0.046 0.187 1557 Planarity : 0.004 0.041 1803 Dihedral : 5.412 56.034 1414 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.73 % Allowed : 18.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.23), residues: 1330 helix: 0.25 (0.24), residues: 478 sheet: -0.43 (0.34), residues: 227 loop : -0.95 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 91 HIS 0.006 0.001 HIS C 182 PHE 0.008 0.001 PHE D 70 TYR 0.022 0.002 TYR A 158 ARG 0.002 0.000 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 403) hydrogen bonds : angle 4.81449 ( 1134) metal coordination : bond 0.00385 ( 27) metal coordination : angle 2.88596 ( 24) covalent geometry : bond 0.00320 (10102) covalent geometry : angle 0.53806 (13726) *********************** 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 175 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 1.536 Fit side-chains REVERT: A 12 GLU cc_start: 0.7582 (pt0) cc_final: 0.7275 (pm20) REVERT: A 80 HIS cc_start: 0.6407 (t70) cc_final: 0.6127 (t-90) REVERT: A 328 GLN cc_start: 0.5542 (tm-30) cc_final: 0.5157 (tm-30) REVERT: A 342 MET cc_start: 0.7044 (ptp) cc_final: 0.6385 (ptp) REVERT: B 56 LYS cc_start: 0.8220 (mttp) cc_final: 0.7985 (mttt) REVERT: B 309 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7772 (mtpp) REVERT: C 151 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7940 (mp) REVERT: D 26 GLU cc_start: 0.6047 (OUTLIER) cc_final: 0.5748 (tm-30) REVERT: D 111 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7116 (mp0) REVERT: D 230 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6894 (mtt180) REVERT: D 313 THR cc_start: 0.7886 (OUTLIER) cc_final: 0.7510 (m) REVERT: D 342 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6174 (mtm) outliers start: 28 outliers final: 18 residues processed: 165 average time/residue: 1.2179 time to fit residues: 219.3276 Evaluate side-chains 172 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 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 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 291 ILE Chi-restraints excluded: chain C residue 292 VAL 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 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 39 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS ** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.134708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.117248 restraints weight = 11342.805| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.25 r_work: 0.3224 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1813 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= 0.144 Angle : 0.555 6.933 13750 Z= 0.277 Chirality : 0.047 0.183 1557 Planarity : 0.004 0.045 1803 Dihedral : 5.437 55.883 1414 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.93 % Allowed : 18.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.23), residues: 1330 helix: 0.21 (0.23), residues: 478 sheet: -0.46 (0.34), residues: 227 loop : -0.95 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 91 HIS 0.006 0.001 HIS C 182 PHE 0.009 0.001 PHE D 70 TYR 0.021 0.002 TYR A 158 ARG 0.002 0.000 ARG B 259 Details of bonding type rmsd hydrogen bonds : bond 0.03510 ( 403) hydrogen bonds : angle 4.83586 ( 1134) metal coordination : bond 0.00404 ( 27) metal coordination : angle 2.92221 ( 24) covalent geometry : bond 0.00333 (10102) covalent geometry : angle 0.54140 (13726) ********************** 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 184 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 1.271 Fit side-chains REVERT: A 12 GLU cc_start: 0.7592 (pt0) cc_final: 0.7289 (pm20) REVERT: A 23 PRO cc_start: 0.7206 (Cg_exo) cc_final: 0.6949 (Cg_endo) REVERT: A 80 HIS cc_start: 0.6405 (t70) cc_final: 0.6132 (t-90) REVERT: A 328 GLN cc_start: 0.5540 (tm-30) cc_final: 0.5141 (tm-30) REVERT: A 342 MET cc_start: 0.7065 (ptp) cc_final: 0.6441 (ptp) REVERT: B 56 LYS cc_start: 0.8236 (mttp) cc_final: 0.8001 (mttt) REVERT: B 309 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7769 (mtpp) REVERT: C 151 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7950 (mp) REVERT: D 26 GLU cc_start: 0.6065 (OUTLIER) cc_final: 0.5772 (tm-30) REVERT: D 111 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7123 (mp0) REVERT: D 230 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6889 (mtt180) REVERT: D 313 THR cc_start: 0.7906 (OUTLIER) cc_final: 0.7527 (m) outliers start: 30 outliers final: 20 residues processed: 175 average time/residue: 1.2455 time to fit residues: 236.7782 Evaluate side-chains 173 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 1.697 ------------------------------------------------------------------------------- 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 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 291 ILE Chi-restraints excluded: chain C residue 292 VAL 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 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 8 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 105 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 315 HIS ** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.134895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.117589 restraints weight = 11349.664| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.24 r_work: 0.3230 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10129 Z= 0.135 Angle : 0.550 6.891 13750 Z= 0.274 Chirality : 0.046 0.182 1557 Planarity : 0.004 0.052 1803 Dihedral : 5.393 56.028 1414 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.44 % Allowed : 18.93 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.23), residues: 1330 helix: 0.24 (0.23), residues: 478 sheet: -0.34 (0.34), residues: 211 loop : -0.95 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 91 HIS 0.006 0.001 HIS C 182 PHE 0.008 0.001 PHE D 70 TYR 0.019 0.002 TYR A 158 ARG 0.002 0.000 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 403) hydrogen bonds : angle 4.80579 ( 1134) metal coordination : bond 0.00372 ( 27) metal coordination : angle 2.86929 ( 24) covalent geometry : bond 0.00310 (10102) covalent geometry : angle 0.53679 (13726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7322.16 seconds wall clock time: 130 minutes 22.63 seconds (7822.63 seconds total)