Starting phenix.real_space_refine on Mon Aug 25 15:38:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c5z_16445/08_2025/8c5z_16445.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c5z_16445/08_2025/8c5z_16445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8c5z_16445/08_2025/8c5z_16445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c5z_16445/08_2025/8c5z_16445.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c5z_16445/08_2025/8c5z_16445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c5z_16445/08_2025/8c5z_16445.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15650 atoms to isotropic. 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 4 6.06 5 S 49 5.16 5 C 10603 2.51 5 N 2825 2.21 5 O 3134 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16615 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2837 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 14, 'TRANS': 338} Chain breaks: 1 Chain: "B" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1474 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "C" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 919 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "D" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1408 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain: "E" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1474 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "F" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 919 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "G" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1408 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain: "H" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1474 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "I" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 919 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "J" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1408 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain: "K" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1474 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "L" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 897 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1715 SG CYS A 218 79.987 32.891 94.445 1.00 93.17 S ATOM 1737 SG CYS A 221 77.516 30.716 96.246 1.00 89.99 S ATOM 1859 SG CYS A 236 80.913 31.491 97.883 1.00 89.99 S ATOM 5516 SG CYS D 218 24.729 50.501 14.031 1.00247.06 S ATOM 5538 SG CYS D 221 27.606 51.827 12.165 1.00253.91 S ATOM 5660 SG CYS D 236 24.206 53.714 12.090 1.00271.18 S ATOM 9317 SG CYS G 218 83.762 106.958 59.518 1.00250.81 S ATOM 9339 SG CYS G 221 81.281 109.065 57.608 1.00243.72 S ATOM 9461 SG CYS G 236 84.384 107.630 55.798 1.00262.56 S ATOM 13118 SG CYS J 218 21.839 83.167 146.406 1.00200.54 S ATOM 13140 SG CYS J 221 24.129 80.503 147.875 1.00223.35 S ATOM 13262 SG CYS J 236 20.385 79.733 147.138 1.00224.74 S Time building chain proxies: 3.42, per 1000 atoms: 0.21 Number of scatterers: 16615 At special positions: 0 Unit cell: (104.92, 124.7, 161.68, 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 4 29.99 S 49 16.00 O 3134 8.00 N 2825 7.00 C 10603 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: 1.42 Conformation dependent library (CDL) restraints added in 590.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 500 " pdb="ZN ZN A 500 " - pdb=" ND1 HIS A 239 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 218 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 221 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 236 " pdb=" ZN D 500 " pdb="ZN ZN D 500 " - pdb=" ND1 HIS D 239 " pdb="ZN ZN D 500 " - pdb=" SG CYS D 221 " pdb="ZN ZN D 500 " - pdb=" SG CYS D 218 " pdb="ZN ZN D 500 " - pdb=" SG CYS D 236 " pdb=" ZN G 500 " pdb="ZN ZN G 500 " - pdb=" ND1 HIS G 239 " pdb="ZN ZN G 500 " - pdb=" SG CYS G 218 " pdb="ZN ZN G 500 " - pdb=" SG CYS G 221 " pdb="ZN ZN G 500 " - pdb=" SG CYS G 236 " pdb=" ZN J 500 " pdb="ZN ZN J 500 " - pdb=" ND1 HIS J 239 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 218 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 236 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 221 " Number of angles added : 12 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3788 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 21 sheets defined 34.1% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 20 through 35 removed outlier: 3.638A pdb=" N MET A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU A 33 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 52 Processing helix chain 'A' and resid 54 through 58 removed outlier: 4.611A pdb=" N GLU A 57 " --> pdb=" O ASP A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 77 Processing helix chain 'A' and resid 122 through 128 Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.599A pdb=" N GLU A 172 " --> pdb=" O PRO A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 275 Processing helix chain 'A' and resid 277 through 290 removed outlier: 3.899A pdb=" N ILE A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 306 removed outlier: 3.758A pdb=" N GLU A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 removed outlier: 4.125A pdb=" N ILE A 310 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 311 " --> pdb=" O TYR A 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 307 through 311' Processing helix chain 'A' and resid 341 through 356 Processing helix chain 'B' and resid 11 through 16 Processing helix chain 'B' and resid 80 through 87 removed outlier: 3.686A pdb=" N LYS B 83 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 150 removed outlier: 4.173A pdb=" N GLU B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE B 146 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 Processing helix chain 'B' and resid 168 through 181 Processing helix chain 'C' and resid 15 through 19 Processing helix chain 'C' and resid 93 through 112 Proline residue: C 109 - end of helix Processing helix chain 'D' and resid 189 through 193 Processing helix chain 'D' and resid 267 through 275 removed outlier: 3.528A pdb=" N GLU D 271 " --> pdb=" O GLY D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 290 removed outlier: 3.588A pdb=" N ILE D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 307 Processing helix chain 'D' and resid 341 through 356 Processing helix chain 'E' and resid 11 through 17 Processing helix chain 'E' and resid 81 through 86 removed outlier: 3.943A pdb=" N ALA E 85 " --> pdb=" O ASP E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 150 removed outlier: 3.645A pdb=" N TRP E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE E 146 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR E 150 " --> pdb=" O ILE E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 167 through 181 removed outlier: 4.137A pdb=" N GLU E 171 " --> pdb=" O GLU E 167 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET E 181 " --> pdb=" O TYR E 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 19 Processing helix chain 'F' and resid 94 through 112 Proline residue: F 109 - end of helix removed outlier: 4.161A pdb=" N GLU F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 193 Processing helix chain 'G' and resid 267 through 275 Processing helix chain 'G' and resid 277 through 290 Processing helix chain 'G' and resid 294 through 306 removed outlier: 3.568A pdb=" N GLU G 306 " --> pdb=" O LEU G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 311 removed outlier: 4.106A pdb=" N ILE G 310 " --> pdb=" O PHE G 307 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE G 311 " --> pdb=" O TYR G 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 307 through 311' Processing helix chain 'G' and resid 340 through 356 removed outlier: 3.502A pdb=" N GLU G 344 " --> pdb=" O ASP G 340 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 17 Processing helix chain 'H' and resid 80 through 87 removed outlier: 3.958A pdb=" N LYS H 83 " --> pdb=" O ASP H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 151 removed outlier: 4.349A pdb=" N GLU H 145 " --> pdb=" O LYS H 141 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE H 146 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR H 150 " --> pdb=" O ILE H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 163 Processing helix chain 'H' and resid 166 through 181 removed outlier: 4.269A pdb=" N LEU H 170 " --> pdb=" O GLU H 166 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU H 171 " --> pdb=" O GLU H 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 19 Processing helix chain 'I' and resid 93 through 112 removed outlier: 3.760A pdb=" N LEU I 97 " --> pdb=" O ASP I 93 " (cutoff:3.500A) Proline residue: I 109 - end of helix Processing helix chain 'J' and resid 189 through 193 Processing helix chain 'J' and resid 267 through 275 Processing helix chain 'J' and resid 277 through 290 removed outlier: 3.691A pdb=" N ILE J 281 " --> pdb=" O SER J 277 " (cutoff:3.500A) Processing helix chain 'J' and resid 294 through 307 Processing helix chain 'J' and resid 340 through 356 removed outlier: 3.508A pdb=" N GLU J 344 " --> pdb=" O ASP J 340 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 17 Processing helix chain 'K' and resid 81 through 86 removed outlier: 4.106A pdb=" N ALA K 85 " --> pdb=" O ASP K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 150 removed outlier: 3.536A pdb=" N TRP K 122 " --> pdb=" O HIS K 118 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU K 145 " --> pdb=" O LYS K 141 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE K 146 " --> pdb=" O ILE K 142 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR K 150 " --> pdb=" O ILE K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 164 Processing helix chain 'K' and resid 167 through 181 removed outlier: 3.800A pdb=" N GLU K 171 " --> pdb=" O GLU K 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 15 through 19 removed outlier: 3.663A pdb=" N ILE L 19 " --> pdb=" O ILE L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 114 Proline residue: L 109 - end of helix removed outlier: 3.745A pdb=" N GLU L 112 " --> pdb=" O LEU L 108 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY L 113 " --> pdb=" O PRO L 109 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU L 114 " --> pdb=" O ARG L 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 87 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 79 through 87 current: chain 'A' and resid 100 through 109 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 114 through 120 current: chain 'A' and resid 152 through 156 Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 217 removed outlier: 6.481A pdb=" N ALA A 207 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ASP A 255 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL A 209 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY A 253 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N TYR A 260 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N LEU A 331 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ARG A 262 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ALA A 333 " --> pdb=" O ARG A 262 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR A 264 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER A 335 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N PHE A 266 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N GLU A 337 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG A 318 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TRP A 336 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A 316 " --> pdb=" O TRP A 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 226 through 227 removed outlier: 3.695A pdb=" N ASP A 226 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 9 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 42 through 49 current: chain 'B' and resid 61 through 67 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 72 through 78 current: chain 'B' and resid 107 through 116 Processing sheet with id=AA5, first strand: chain 'B' and resid 19 through 21 Processing sheet with id=AA6, first strand: chain 'C' and resid 12 through 13 removed outlier: 7.057A pdb=" N VAL C 12 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N ILE C 29 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL C 65 " --> pdb=" O ASP C 88 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ASP C 88 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG C 67 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE C 86 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE C 69 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ILE C 79 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE C 52 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS C 34 " --> pdb=" O TRP C 43 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASP C 45 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N VAL C 32 " --> pdb=" O ASP C 45 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 186 through 187 removed outlier: 6.344A pdb=" N THR D 186 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N ARG D 203 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 9.187A pdb=" N GLU D 314 " --> pdb=" O ASP D 338 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ASP D 338 " --> pdb=" O GLU D 314 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL D 316 " --> pdb=" O TRP D 336 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N TRP D 336 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ARG D 318 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N TYR D 260 " --> pdb=" O LEU D 329 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N LEU D 331 " --> pdb=" O TYR D 260 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARG D 262 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ALA D 333 " --> pdb=" O ARG D 262 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR D 264 " --> pdb=" O ALA D 333 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N SER D 335 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N PHE D 266 " --> pdb=" O SER D 335 " (cutoff:3.500A) removed outlier: 11.298A pdb=" N GLU D 337 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLY D 253 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N VAL D 209 " --> pdb=" O GLY D 253 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ASP D 255 " --> pdb=" O ALA D 207 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA D 207 " --> pdb=" O ASP D 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 226 through 228 Processing sheet with id=AA9, first strand: chain 'E' and resid 8 through 9 removed outlier: 6.628A pdb=" N GLN E 95 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL E 114 " --> pdb=" O GLN E 95 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE E 97 " --> pdb=" O GLU E 112 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL E 72 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ILE E 109 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TRP E 74 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL E 111 " --> pdb=" O TRP E 74 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU E 76 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLY E 113 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 11.750A pdb=" N PHE E 78 " --> pdb=" O GLY E 113 " (cutoff:3.500A) removed outlier: 15.781A pdb=" N SER E 115 " --> pdb=" O PHE E 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 19 through 21 Processing sheet with id=AB2, first strand: chain 'F' and resid 12 through 13 removed outlier: 6.537A pdb=" N VAL F 12 " --> pdb=" O SER F 27 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N ILE F 29 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL F 65 " --> pdb=" O ASP F 88 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ASP F 88 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG F 67 " --> pdb=" O ILE F 86 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE F 86 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE F 69 " --> pdb=" O GLU F 84 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS F 80 " --> pdb=" O ILE F 73 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N ILE F 79 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE F 52 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N MET F 41 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N VAL F 35 " --> pdb=" O MET F 41 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N TRP F 43 " --> pdb=" O ILE F 33 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 186 through 187 removed outlier: 6.073A pdb=" N THR G 186 " --> pdb=" O GLU G 201 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ARG G 203 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL G 316 " --> pdb=" O TRP G 336 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N TRP G 336 " --> pdb=" O VAL G 316 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ARG G 318 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N TYR G 260 " --> pdb=" O LEU G 329 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N LEU G 331 " --> pdb=" O TYR G 260 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARG G 262 " --> pdb=" O LEU G 331 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA G 333 " --> pdb=" O ARG G 262 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR G 264 " --> pdb=" O ALA G 333 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N SER G 335 " --> pdb=" O THR G 264 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N PHE G 266 " --> pdb=" O SER G 335 " (cutoff:3.500A) removed outlier: 11.940A pdb=" N GLU G 337 " --> pdb=" O PHE G 266 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY G 253 " --> pdb=" O VAL G 209 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL G 209 " --> pdb=" O GLY G 253 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ASP G 255 " --> pdb=" O ALA G 207 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ALA G 207 " --> pdb=" O ASP G 255 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 226 through 228 removed outlier: 3.510A pdb=" N VAL G 233 " --> pdb=" O ASP G 228 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 7 through 9 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 42 through 49 current: chain 'H' and resid 61 through 67 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 72 through 78 current: chain 'H' and resid 106 through 116 Processing sheet with id=AB6, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AB7, first strand: chain 'I' and resid 12 through 13 removed outlier: 3.567A pdb=" N VAL I 12 " --> pdb=" O ARG I 25 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER I 27 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL I 65 " --> pdb=" O ASP I 88 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ASP I 88 " --> pdb=" O VAL I 65 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG I 67 " --> pdb=" O ILE I 86 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE I 86 " --> pdb=" O ARG I 67 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE I 69 " --> pdb=" O GLU I 84 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS I 80 " --> pdb=" O ILE I 73 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N VAL I 50 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N ILE I 81 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE I 52 " --> pdb=" O ILE I 81 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA I 83 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS I 34 " --> pdb=" O TRP I 43 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP I 45 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL I 32 " --> pdb=" O ASP I 45 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 186 through 187 removed outlier: 6.035A pdb=" N THR J 186 " --> pdb=" O GLU J 201 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ARG J 203 " --> pdb=" O THR J 186 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL J 316 " --> pdb=" O TRP J 336 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N TRP J 336 " --> pdb=" O VAL J 316 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ARG J 318 " --> pdb=" O SER J 334 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N TYR J 260 " --> pdb=" O LEU J 329 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N LEU J 331 " --> pdb=" O TYR J 260 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ARG J 262 " --> pdb=" O LEU J 331 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA J 333 " --> pdb=" O ARG J 262 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR J 264 " --> pdb=" O ALA J 333 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N SER J 335 " --> pdb=" O THR J 264 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N PHE J 266 " --> pdb=" O SER J 335 " (cutoff:3.500A) removed outlier: 11.149A pdb=" N GLU J 337 " --> pdb=" O PHE J 266 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE J 245 " --> pdb=" O ASP J 216 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASP J 216 " --> pdb=" O ILE J 245 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N MET J 247 " --> pdb=" O THR J 214 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR J 214 " --> pdb=" O MET J 247 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE J 249 " --> pdb=" O VAL J 212 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL J 212 " --> pdb=" O ILE J 249 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASP J 251 " --> pdb=" O TYR J 210 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS J 208 " --> pdb=" O GLY J 253 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP J 255 " --> pdb=" O ILE J 206 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE J 206 " --> pdb=" O ASP J 255 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 226 through 228 removed outlier: 3.603A pdb=" N VAL J 233 " --> pdb=" O ASP J 228 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 8 through 9 removed outlier: 6.365A pdb=" N THR K 8 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N VAL K 46 " --> pdb=" O THR K 8 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 43 through 49 current: chain 'K' and resid 61 through 67 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 72 through 78 current: chain 'K' and resid 106 through 116 Processing sheet with id=AC2, first strand: chain 'K' and resid 19 through 21 Processing sheet with id=AC3, first strand: chain 'L' and resid 12 through 13 removed outlier: 6.839A pdb=" N VAL L 12 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N ILE L 29 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL L 65 " --> pdb=" O ASP L 88 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ASP L 88 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG L 67 " --> pdb=" O ILE L 86 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE L 86 " --> pdb=" O ARG L 67 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE L 69 " --> pdb=" O GLU L 84 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N HIS L 80 " --> pdb=" O ILE L 73 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASN L 75 " --> pdb=" O GLY L 78 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY L 78 " --> pdb=" O ASN L 75 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N ILE L 79 " --> pdb=" O VAL L 50 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ILE L 52 " --> pdb=" O ILE L 79 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA L 83 " --> pdb=" O GLU L 54 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N MET L 41 " --> pdb=" O VAL L 35 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N VAL L 35 " --> pdb=" O MET L 41 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N TRP L 43 " --> pdb=" O ILE L 33 " (cutoff:3.500A) 696 hydrogen bonds defined for protein. 1926 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 1.86 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: 5510 1.34 - 1.46: 3400 1.46 - 1.58: 7867 1.58 - 1.70: 0 1.70 - 1.82: 86 Bond restraints: 16863 Sorted by residual: bond pdb=" N ALA L 92 " pdb=" CA ALA L 92 " ideal model delta sigma weight residual 1.453 1.496 -0.043 1.27e-02 6.20e+03 1.13e+01 bond pdb=" CA ALA L 92 " pdb=" C ALA L 92 " ideal model delta sigma weight residual 1.528 1.561 -0.034 1.33e-02 5.65e+03 6.35e+00 bond pdb=" N ASP L 93 " pdb=" CA ASP L 93 " ideal model delta sigma weight residual 1.455 1.481 -0.027 1.36e-02 5.41e+03 3.81e+00 bond pdb=" CG GLU A 283 " pdb=" CD GLU A 283 " ideal model delta sigma weight residual 1.516 1.480 0.036 2.50e-02 1.60e+03 2.07e+00 bond pdb=" CG GLU J 290 " pdb=" CD GLU J 290 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.86e+00 ... (remaining 16858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 22399 2.65 - 5.29: 258 5.29 - 7.94: 22 7.94 - 10.59: 2 10.59 - 13.23: 2 Bond angle restraints: 22683 Sorted by residual: angle pdb=" N ALA L 92 " pdb=" CA ALA L 92 " pdb=" C ALA L 92 " ideal model delta sigma weight residual 110.35 121.26 -10.91 1.38e+00 5.25e-01 6.25e+01 angle pdb=" C ARG K 79 " pdb=" CA ARG K 79 " pdb=" CB ARG K 79 " ideal model delta sigma weight residual 117.23 108.19 9.04 1.36e+00 5.41e-01 4.42e+01 angle pdb=" CA ARG K 79 " pdb=" C ARG K 79 " pdb=" N ASP K 80 " ideal model delta sigma weight residual 119.98 115.76 4.22 8.50e-01 1.38e+00 2.46e+01 angle pdb=" C GLU J 289 " pdb=" N GLU J 290 " pdb=" CA GLU J 290 " ideal model delta sigma weight residual 121.18 113.30 7.88 1.98e+00 2.55e-01 1.58e+01 angle pdb=" N GLU A 283 " pdb=" CA GLU A 283 " pdb=" CB GLU A 283 " ideal model delta sigma weight residual 110.28 116.30 -6.02 1.55e+00 4.16e-01 1.51e+01 ... (remaining 22678 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 9270 18.01 - 36.01: 917 36.01 - 54.02: 137 54.02 - 72.03: 16 72.03 - 90.03: 18 Dihedral angle restraints: 10358 sinusoidal: 4456 harmonic: 5902 Sorted by residual: dihedral pdb=" CA LEU C 107 " pdb=" C LEU C 107 " pdb=" N LEU C 108 " pdb=" CA LEU C 108 " ideal model delta harmonic sigma weight residual -180.00 -156.46 -23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA PHE J 266 " pdb=" C PHE J 266 " pdb=" N GLY J 267 " pdb=" CA GLY J 267 " ideal model delta harmonic sigma weight residual 180.00 157.68 22.32 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA LEU L 107 " pdb=" C LEU L 107 " pdb=" N LEU L 108 " pdb=" CA LEU L 108 " ideal model delta harmonic sigma weight residual -180.00 -158.92 -21.08 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 10355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2170 0.074 - 0.148: 357 0.148 - 0.223: 9 0.223 - 0.297: 0 0.297 - 0.371: 1 Chirality restraints: 2537 Sorted by residual: chirality pdb=" CA TYR A 341 " pdb=" N TYR A 341 " pdb=" C TYR A 341 " pdb=" CB TYR A 341 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CA GLU J 289 " pdb=" N GLU J 289 " pdb=" C GLU J 289 " pdb=" CB GLU J 289 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CA ARG A 102 " pdb=" N ARG A 102 " pdb=" C ARG A 102 " pdb=" CB ARG A 102 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.76e-01 ... (remaining 2534 not shown) Planarity restraints: 2890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 108 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.97e+00 pdb=" N PRO F 109 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO F 109 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 109 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 122 " 0.013 2.00e-02 2.50e+03 1.16e-02 3.39e+00 pdb=" CG TRP K 122 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP K 122 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP K 122 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP K 122 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP K 122 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP K 122 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 122 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 122 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP K 122 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 26 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C ASP E 26 " -0.031 2.00e-02 2.50e+03 pdb=" O ASP E 26 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE E 27 " 0.010 2.00e-02 2.50e+03 ... (remaining 2887 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 226 2.63 - 3.20: 14959 3.20 - 3.77: 25147 3.77 - 4.33: 33407 4.33 - 4.90: 54388 Nonbonded interactions: 128127 Sorted by model distance: nonbonded pdb=" CD2 TYR A 341 " pdb=" CB ASN B 120 " model vdw 2.063 3.740 nonbonded pdb=" OE1 GLU J 350 " pdb=" NZ LYS J 354 " model vdw 2.136 3.120 nonbonded pdb=" O THR H 153 " pdb=" OG SER H 156 " model vdw 2.144 3.040 nonbonded pdb=" O LEU G 288 " pdb=" OG SER G 291 " model vdw 2.153 3.040 nonbonded pdb=" OG SER A 277 " pdb=" OE1 GLU A 280 " model vdw 2.157 3.040 ... (remaining 128122 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 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = (chain 'C' and resid 8 through 117) selection = (chain 'F' and resid 8 through 117) selection = (chain 'I' and resid 8 through 117) selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' } 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 group one per residue 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: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.470 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 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 0.068 16879 Z= 0.181 Angle : 0.705 13.235 22695 Z= 0.394 Chirality : 0.050 0.371 2537 Planarity : 0.004 0.056 2890 Dihedral : 14.174 90.034 6570 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.07 % Favored : 96.68 % Rotamer: Outliers : 0.17 % Allowed : 0.22 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.18), residues: 2018 helix: 0.96 (0.21), residues: 593 sheet: -0.29 (0.21), residues: 576 loop : -0.50 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 4 TYR 0.020 0.002 TYR H 127 PHE 0.021 0.002 PHE J 252 TRP 0.032 0.002 TRP K 122 HIS 0.005 0.001 HIS D 239 Details of bonding type rmsd covalent geometry : bond 0.00393 (16863) covalent geometry : angle 0.70158 (22683) hydrogen bonds : bond 0.14482 ( 696) hydrogen bonds : angle 6.84204 ( 1926) metal coordination : bond 0.02122 ( 16) metal coordination : angle 2.94002 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 383 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8469 (tm-30) REVERT: A 128 TYR cc_start: 0.8420 (t80) cc_final: 0.8213 (t80) REVERT: A 293 LEU cc_start: 0.8585 (mm) cc_final: 0.7893 (mp) REVERT: A 320 ASN cc_start: 0.8291 (t0) cc_final: 0.8087 (t0) REVERT: B 171 GLU cc_start: 0.8895 (pm20) cc_final: 0.8662 (pm20) REVERT: C 41 MET cc_start: 0.6128 (tmm) cc_final: 0.5314 (tmm) REVERT: C 58 ASP cc_start: 0.8036 (t0) cc_final: 0.7134 (m-30) REVERT: C 59 LEU cc_start: 0.6417 (mt) cc_final: 0.4947 (mt) REVERT: C 102 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8896 (tm-30) REVERT: D 265 LEU cc_start: 0.8021 (tp) cc_final: 0.7745 (tp) REVERT: D 295 THR cc_start: 0.8252 (p) cc_final: 0.7729 (t) REVERT: E 181 MET cc_start: 0.6464 (mpp) cc_final: 0.5543 (ttm) REVERT: F 36 ASP cc_start: 0.5628 (p0) cc_final: 0.3775 (p0) REVERT: F 75 ASN cc_start: 0.7603 (m110) cc_final: 0.7277 (p0) REVERT: H 80 ASP cc_start: 0.8615 (t70) cc_final: 0.8385 (t0) REVERT: H 176 LEU cc_start: 0.8951 (tt) cc_final: 0.8459 (tt) REVERT: I 39 ASP cc_start: 0.8485 (m-30) cc_final: 0.8243 (m-30) REVERT: I 106 LYS cc_start: 0.9314 (tmtt) cc_final: 0.9088 (tmtt) REVERT: J 358 MET cc_start: 0.1608 (mpp) cc_final: 0.1070 (mpp) REVERT: K 8 THR cc_start: 0.8939 (m) cc_final: 0.8699 (p) REVERT: K 67 ASP cc_start: 0.7910 (t70) cc_final: 0.7481 (p0) REVERT: K 112 GLU cc_start: 0.7713 (tp30) cc_final: 0.7359 (mm-30) REVERT: K 132 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7822 (mt-10) REVERT: K 155 LYS cc_start: 0.8303 (mppt) cc_final: 0.7913 (mmmt) REVERT: L 41 MET cc_start: 0.5843 (tmm) cc_final: 0.5558 (tmm) REVERT: L 43 TRP cc_start: 0.7648 (m-90) cc_final: 0.6530 (m-90) REVERT: L 59 LEU cc_start: 0.6279 (mm) cc_final: 0.4826 (pt) REVERT: L 82 TYR cc_start: 0.6748 (t80) cc_final: 0.6409 (m-10) REVERT: L 94 LEU cc_start: 0.8785 (pp) cc_final: 0.8293 (pp) REVERT: L 97 LEU cc_start: 0.8943 (tt) cc_final: 0.8440 (tt) outliers start: 3 outliers final: 2 residues processed: 385 average time/residue: 0.1630 time to fit residues: 88.1058 Evaluate side-chains 220 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 218 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 341 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN B 149 GLN H 149 GLN ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 GLN ** L 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.132046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.090882 restraints weight = 45352.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.093604 restraints weight = 25669.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.095417 restraints weight = 18794.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.096378 restraints weight = 15850.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.096785 restraints weight = 14481.054| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16879 Z= 0.151 Angle : 0.659 8.746 22695 Z= 0.348 Chirality : 0.049 0.180 2537 Planarity : 0.004 0.050 2890 Dihedral : 5.147 53.802 2276 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.37 % Favored : 96.43 % Rotamer: Outliers : 1.34 % Allowed : 11.30 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.18), residues: 2018 helix: 0.78 (0.20), residues: 616 sheet: -0.46 (0.21), residues: 560 loop : -0.56 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 4 TYR 0.017 0.002 TYR J 308 PHE 0.022 0.002 PHE A 326 TRP 0.021 0.001 TRP K 122 HIS 0.009 0.002 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00346 (16863) covalent geometry : angle 0.65592 (22683) hydrogen bonds : bond 0.04594 ( 696) hydrogen bonds : angle 5.55577 ( 1926) metal coordination : bond 0.01427 ( 16) metal coordination : angle 2.80507 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 252 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8400 (tm-30) REVERT: A 128 TYR cc_start: 0.8061 (t80) cc_final: 0.7832 (t80) REVERT: A 320 ASN cc_start: 0.8420 (t0) cc_final: 0.8094 (t0) REVERT: C 41 MET cc_start: 0.5764 (tmm) cc_final: 0.5517 (tmm) REVERT: C 42 PHE cc_start: 0.7784 (p90) cc_final: 0.7303 (p90) REVERT: C 58 ASP cc_start: 0.7468 (t0) cc_final: 0.6655 (m-30) REVERT: D 265 LEU cc_start: 0.8249 (tp) cc_final: 0.8015 (tp) REVERT: D 295 THR cc_start: 0.8384 (p) cc_final: 0.7860 (t) REVERT: E 177 TYR cc_start: 0.8219 (t80) cc_final: 0.7989 (t80) REVERT: E 181 MET cc_start: 0.6210 (mpp) cc_final: 0.4975 (ttm) REVERT: H 121 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7594 (mmt) REVERT: J 223 LYS cc_start: 0.7165 (tptp) cc_final: 0.6918 (mmtt) REVERT: J 265 LEU cc_start: 0.7321 (tp) cc_final: 0.7115 (tt) REVERT: K 132 GLU cc_start: 0.8531 (mm-30) cc_final: 0.7964 (mt-10) REVERT: K 155 LYS cc_start: 0.8159 (mppt) cc_final: 0.7786 (mmmt) REVERT: L 43 TRP cc_start: 0.7627 (m-90) cc_final: 0.7012 (m-90) REVERT: L 82 TYR cc_start: 0.6959 (t80) cc_final: 0.6657 (m-10) outliers start: 24 outliers final: 14 residues processed: 267 average time/residue: 0.1489 time to fit residues: 58.5165 Evaluate side-chains 218 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 127 TYR Chi-restraints excluded: chain J residue 186 THR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 80 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 173 optimal weight: 8.9990 chunk 174 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 194 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 196 optimal weight: 9.9990 chunk 58 optimal weight: 0.0370 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.132259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.101160 restraints weight = 45499.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.099564 restraints weight = 31801.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.100584 restraints weight = 30959.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.101078 restraints weight = 21924.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.102164 restraints weight = 20168.504| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16879 Z= 0.119 Angle : 0.597 7.951 22695 Z= 0.313 Chirality : 0.048 0.181 2537 Planarity : 0.004 0.047 2890 Dihedral : 4.920 48.109 2274 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.73 % Favored : 97.08 % Rotamer: Outliers : 1.62 % Allowed : 13.98 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.18), residues: 2018 helix: 0.85 (0.20), residues: 616 sheet: -0.38 (0.21), residues: 576 loop : -0.59 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 71 TYR 0.017 0.001 TYR J 308 PHE 0.017 0.001 PHE J 252 TRP 0.031 0.002 TRP I 117 HIS 0.007 0.001 HIS K 136 Details of bonding type rmsd covalent geometry : bond 0.00266 (16863) covalent geometry : angle 0.59498 (22683) hydrogen bonds : bond 0.04013 ( 696) hydrogen bonds : angle 5.17195 ( 1926) metal coordination : bond 0.01433 ( 16) metal coordination : angle 2.38762 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 244 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8381 (ttmt) cc_final: 0.8060 (ttpt) REVERT: A 320 ASN cc_start: 0.8378 (t0) cc_final: 0.8016 (t0) REVERT: C 41 MET cc_start: 0.5943 (tmm) cc_final: 0.5652 (tmm) REVERT: C 42 PHE cc_start: 0.7977 (p90) cc_final: 0.7491 (p90) REVERT: D 265 LEU cc_start: 0.8160 (tp) cc_final: 0.7934 (tp) REVERT: D 295 THR cc_start: 0.8367 (p) cc_final: 0.7829 (t) REVERT: E 177 TYR cc_start: 0.8276 (t80) cc_final: 0.7913 (t80) REVERT: E 180 MET cc_start: 0.7890 (mmm) cc_final: 0.7633 (mmt) REVERT: E 181 MET cc_start: 0.6111 (mpp) cc_final: 0.4868 (ttm) REVERT: F 39 ASP cc_start: 0.8609 (t0) cc_final: 0.8244 (p0) REVERT: G 271 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7316 (pm20) REVERT: K 155 LYS cc_start: 0.8073 (mppt) cc_final: 0.7712 (mmmt) outliers start: 29 outliers final: 15 residues processed: 261 average time/residue: 0.1390 time to fit residues: 54.6666 Evaluate side-chains 231 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 215 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain J residue 186 THR Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 80 HIS Chi-restraints excluded: chain L residue 93 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 89 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 145 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 162 ASN ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.130352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.099979 restraints weight = 45245.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.098495 restraints weight = 33255.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.099153 restraints weight = 32398.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.099344 restraints weight = 22768.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.099914 restraints weight = 20468.241| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16879 Z= 0.170 Angle : 0.629 10.646 22695 Z= 0.326 Chirality : 0.048 0.226 2537 Planarity : 0.004 0.045 2890 Dihedral : 4.914 48.669 2274 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.32 % Favored : 96.48 % Rotamer: Outliers : 2.35 % Allowed : 16.22 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.18), residues: 2018 helix: 0.84 (0.20), residues: 619 sheet: -0.49 (0.21), residues: 573 loop : -0.64 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 79 TYR 0.015 0.002 TYR J 308 PHE 0.016 0.002 PHE J 252 TRP 0.014 0.001 TRP I 117 HIS 0.006 0.001 HIS B 136 Details of bonding type rmsd covalent geometry : bond 0.00400 (16863) covalent geometry : angle 0.62657 (22683) hydrogen bonds : bond 0.04161 ( 696) hydrogen bonds : angle 5.16812 ( 1926) metal coordination : bond 0.00914 ( 16) metal coordination : angle 2.48413 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 226 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 MET cc_start: 0.7895 (tpp) cc_final: 0.7375 (tpp) REVERT: C 41 MET cc_start: 0.6122 (tmm) cc_final: 0.5917 (tmm) REVERT: D 265 LEU cc_start: 0.8154 (tp) cc_final: 0.7920 (tp) REVERT: D 295 THR cc_start: 0.8463 (p) cc_final: 0.7904 (t) REVERT: E 177 TYR cc_start: 0.8342 (t80) cc_final: 0.8043 (t80) REVERT: E 181 MET cc_start: 0.6276 (mpp) cc_final: 0.4876 (ttm) REVERT: G 271 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7389 (pm20) REVERT: G 358 MET cc_start: 0.7884 (mmp) cc_final: 0.7629 (mmp) REVERT: H 58 ASP cc_start: 0.6668 (p0) cc_final: 0.6426 (p0) REVERT: J 264 THR cc_start: 0.7958 (m) cc_final: 0.7659 (p) REVERT: K 103 TRP cc_start: 0.8064 (t60) cc_final: 0.7365 (t60) REVERT: K 132 GLU cc_start: 0.8587 (mm-30) cc_final: 0.7846 (mt-10) REVERT: K 155 LYS cc_start: 0.8065 (mppt) cc_final: 0.7639 (mmmt) REVERT: L 41 MET cc_start: 0.7092 (ptm) cc_final: 0.6880 (ppp) outliers start: 42 outliers final: 23 residues processed: 249 average time/residue: 0.1242 time to fit residues: 48.3948 Evaluate side-chains 220 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 36 TYR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 127 TYR Chi-restraints excluded: chain J residue 186 THR Chi-restraints excluded: chain L residue 59 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 108 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 13 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 75 ASN ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.131638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.101492 restraints weight = 45065.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.099635 restraints weight = 31460.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.100506 restraints weight = 32256.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.101102 restraints weight = 22704.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.102158 restraints weight = 20481.722| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16879 Z= 0.124 Angle : 0.604 9.181 22695 Z= 0.311 Chirality : 0.047 0.172 2537 Planarity : 0.004 0.064 2890 Dihedral : 4.875 55.223 2274 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.87 % Favored : 96.93 % Rotamer: Outliers : 2.35 % Allowed : 17.73 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.18), residues: 2018 helix: 0.95 (0.21), residues: 619 sheet: -0.47 (0.20), residues: 573 loop : -0.62 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 38 TYR 0.016 0.001 TYR J 308 PHE 0.014 0.001 PHE I 42 TRP 0.010 0.001 TRP B 103 HIS 0.005 0.001 HIS K 136 Details of bonding type rmsd covalent geometry : bond 0.00290 (16863) covalent geometry : angle 0.60203 (22683) hydrogen bonds : bond 0.03821 ( 696) hydrogen bonds : angle 5.00701 ( 1926) metal coordination : bond 0.01077 ( 16) metal coordination : angle 2.20097 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 225 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ASN cc_start: 0.8310 (t0) cc_final: 0.8076 (t0) REVERT: B 121 MET cc_start: 0.7822 (tpp) cc_final: 0.7350 (tpp) REVERT: B 181 MET cc_start: 0.8115 (tpp) cc_final: 0.7232 (tpp) REVERT: C 41 MET cc_start: 0.5997 (tmm) cc_final: 0.5786 (tmm) REVERT: D 265 LEU cc_start: 0.8143 (tp) cc_final: 0.7925 (tp) REVERT: D 295 THR cc_start: 0.8460 (p) cc_final: 0.7912 (t) REVERT: E 177 TYR cc_start: 0.8244 (t80) cc_final: 0.7896 (t80) REVERT: E 181 MET cc_start: 0.6104 (mpp) cc_final: 0.4739 (ttm) REVERT: G 271 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7321 (pm20) REVERT: H 26 ASP cc_start: 0.8385 (p0) cc_final: 0.8153 (p0) REVERT: H 58 ASP cc_start: 0.6629 (p0) cc_final: 0.6356 (p0) REVERT: H 127 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.7914 (m-10) REVERT: J 264 THR cc_start: 0.7875 (m) cc_final: 0.7542 (p) REVERT: K 103 TRP cc_start: 0.7966 (t60) cc_final: 0.7389 (t60) REVERT: K 132 GLU cc_start: 0.8560 (mm-30) cc_final: 0.7851 (mt-10) REVERT: K 155 LYS cc_start: 0.7900 (mppt) cc_final: 0.7495 (mmmt) REVERT: L 43 TRP cc_start: 0.7239 (m-90) cc_final: 0.6850 (m-90) REVERT: L 80 HIS cc_start: 0.6932 (OUTLIER) cc_final: 0.6074 (m-70) outliers start: 42 outliers final: 24 residues processed: 253 average time/residue: 0.1246 time to fit residues: 49.3337 Evaluate side-chains 223 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain E residue 36 TYR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 127 TYR Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain J residue 186 THR Chi-restraints excluded: chain L residue 40 TYR Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 80 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 150 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 135 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.129453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.088731 restraints weight = 45176.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.091363 restraints weight = 26042.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.092902 restraints weight = 19120.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.094008 restraints weight = 16178.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.094497 restraints weight = 14770.673| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16879 Z= 0.164 Angle : 0.628 16.714 22695 Z= 0.324 Chirality : 0.048 0.195 2537 Planarity : 0.004 0.043 2890 Dihedral : 4.940 53.207 2274 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.52 % Favored : 96.28 % Rotamer: Outliers : 2.74 % Allowed : 18.46 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.18), residues: 2018 helix: 0.95 (0.21), residues: 619 sheet: -0.53 (0.21), residues: 555 loop : -0.61 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 38 TYR 0.014 0.002 TYR C 40 PHE 0.014 0.002 PHE J 252 TRP 0.008 0.001 TRP J 234 HIS 0.006 0.001 HIS K 136 Details of bonding type rmsd covalent geometry : bond 0.00389 (16863) covalent geometry : angle 0.62566 (22683) hydrogen bonds : bond 0.04120 ( 696) hydrogen bonds : angle 5.07056 ( 1926) metal coordination : bond 0.00741 ( 16) metal coordination : angle 2.22737 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 215 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8594 (ttmt) cc_final: 0.8193 (tttt) REVERT: A 320 ASN cc_start: 0.8520 (t0) cc_final: 0.8272 (t0) REVERT: B 72 VAL cc_start: 0.8712 (t) cc_final: 0.8475 (p) REVERT: B 121 MET cc_start: 0.7996 (tpp) cc_final: 0.7558 (tpp) REVERT: B 180 MET cc_start: 0.7295 (ppp) cc_final: 0.6493 (ppp) REVERT: B 181 MET cc_start: 0.8074 (tpp) cc_final: 0.7413 (mmm) REVERT: D 265 LEU cc_start: 0.8288 (tp) cc_final: 0.8018 (tp) REVERT: D 295 THR cc_start: 0.8544 (p) cc_final: 0.8034 (t) REVERT: E 177 TYR cc_start: 0.8293 (t80) cc_final: 0.7941 (t80) REVERT: E 180 MET cc_start: 0.7497 (mmp) cc_final: 0.7201 (mmp) REVERT: E 181 MET cc_start: 0.6156 (mpp) cc_final: 0.4704 (ttm) REVERT: G 271 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7490 (pm20) REVERT: G 305 ASP cc_start: 0.8010 (t0) cc_final: 0.7723 (t70) REVERT: H 26 ASP cc_start: 0.8544 (p0) cc_final: 0.8315 (p0) REVERT: I 64 GLN cc_start: 0.8078 (pm20) cc_final: 0.7682 (pm20) REVERT: J 264 THR cc_start: 0.8089 (m) cc_final: 0.7685 (p) REVERT: K 103 TRP cc_start: 0.8234 (t60) cc_final: 0.7518 (t60) REVERT: K 155 LYS cc_start: 0.8027 (mppt) cc_final: 0.7556 (mmmt) REVERT: L 41 MET cc_start: 0.7072 (ptm) cc_final: 0.6843 (ppp) REVERT: L 43 TRP cc_start: 0.7725 (m-90) cc_final: 0.7336 (m-90) REVERT: L 80 HIS cc_start: 0.7271 (OUTLIER) cc_final: 0.6647 (m-70) outliers start: 49 outliers final: 28 residues processed: 249 average time/residue: 0.1225 time to fit residues: 48.2095 Evaluate side-chains 228 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 36 TYR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 127 TYR Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain J residue 186 THR Chi-restraints excluded: chain L residue 40 TYR Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 80 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 168 optimal weight: 0.4980 chunk 193 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 163 optimal weight: 0.3980 chunk 192 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 181 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 53 optimal weight: 0.0370 chunk 64 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.131347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.094700 restraints weight = 44844.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.096281 restraints weight = 26545.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.095699 restraints weight = 20365.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.096132 restraints weight = 20423.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.096298 restraints weight = 18876.435| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16879 Z= 0.111 Angle : 0.607 12.958 22695 Z= 0.311 Chirality : 0.048 0.192 2537 Planarity : 0.003 0.042 2890 Dihedral : 4.799 53.619 2274 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.53 % Favored : 97.27 % Rotamer: Outliers : 1.85 % Allowed : 19.74 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.18), residues: 2018 helix: 0.99 (0.21), residues: 619 sheet: -0.46 (0.20), residues: 573 loop : -0.61 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 38 TYR 0.015 0.001 TYR J 308 PHE 0.017 0.001 PHE C 42 TRP 0.011 0.001 TRP E 74 HIS 0.005 0.001 HIS K 136 Details of bonding type rmsd covalent geometry : bond 0.00251 (16863) covalent geometry : angle 0.60528 (22683) hydrogen bonds : bond 0.03684 ( 696) hydrogen bonds : angle 4.90177 ( 1926) metal coordination : bond 0.01166 ( 16) metal coordination : angle 1.99662 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 224 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8417 (tttt) cc_final: 0.7977 (ttmt) REVERT: A 132 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7326 (mm-30) REVERT: A 138 LYS cc_start: 0.8517 (ttmt) cc_final: 0.8200 (tttt) REVERT: A 307 PHE cc_start: 0.7510 (m-80) cc_final: 0.7300 (m-80) REVERT: A 320 ASN cc_start: 0.8457 (t0) cc_final: 0.8201 (t0) REVERT: B 72 VAL cc_start: 0.8567 (t) cc_final: 0.8341 (p) REVERT: B 121 MET cc_start: 0.7732 (tpp) cc_final: 0.7291 (tpp) REVERT: B 180 MET cc_start: 0.7254 (ppp) cc_final: 0.6950 (ppp) REVERT: B 181 MET cc_start: 0.8240 (tpp) cc_final: 0.7477 (mmm) REVERT: C 58 ASP cc_start: 0.7556 (t0) cc_final: 0.6800 (m-30) REVERT: D 265 LEU cc_start: 0.8222 (tp) cc_final: 0.7927 (tp) REVERT: D 283 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8618 (tm-30) REVERT: D 295 THR cc_start: 0.8517 (p) cc_final: 0.7990 (t) REVERT: E 177 TYR cc_start: 0.8410 (t80) cc_final: 0.8032 (t80) REVERT: E 180 MET cc_start: 0.7523 (mmp) cc_final: 0.7266 (mmp) REVERT: E 181 MET cc_start: 0.6073 (mpp) cc_final: 0.4687 (ttm) REVERT: G 271 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7532 (pm20) REVERT: G 305 ASP cc_start: 0.7947 (t0) cc_final: 0.7716 (t70) REVERT: H 127 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7962 (m-10) REVERT: I 64 GLN cc_start: 0.8066 (pm20) cc_final: 0.7603 (pm20) REVERT: J 264 THR cc_start: 0.8160 (m) cc_final: 0.7756 (p) REVERT: K 103 TRP cc_start: 0.8036 (t60) cc_final: 0.7285 (t60) REVERT: K 132 GLU cc_start: 0.8583 (mm-30) cc_final: 0.7916 (mt-10) REVERT: K 155 LYS cc_start: 0.8062 (mppt) cc_final: 0.7621 (mmmt) REVERT: L 43 TRP cc_start: 0.7649 (m-90) cc_final: 0.7288 (m-90) REVERT: L 80 HIS cc_start: 0.7322 (OUTLIER) cc_final: 0.6596 (m-70) outliers start: 33 outliers final: 16 residues processed: 246 average time/residue: 0.1263 time to fit residues: 48.3570 Evaluate side-chains 229 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 209 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain E residue 36 TYR Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 127 TYR Chi-restraints excluded: chain J residue 186 THR Chi-restraints excluded: chain L residue 40 TYR Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 80 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 40 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 97 optimal weight: 0.0770 chunk 113 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 165 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.130809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.094234 restraints weight = 45156.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.095491 restraints weight = 27372.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.094774 restraints weight = 20928.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.095507 restraints weight = 21625.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.096264 restraints weight = 18606.458| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16879 Z= 0.122 Angle : 0.618 12.362 22695 Z= 0.316 Chirality : 0.047 0.171 2537 Planarity : 0.003 0.044 2890 Dihedral : 4.778 53.730 2274 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.17 % Favored : 96.63 % Rotamer: Outliers : 2.40 % Allowed : 19.57 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.18), residues: 2018 helix: 0.96 (0.21), residues: 619 sheet: -0.44 (0.21), residues: 573 loop : -0.61 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 38 TYR 0.016 0.001 TYR A 341 PHE 0.014 0.001 PHE J 252 TRP 0.010 0.001 TRP J 234 HIS 0.005 0.001 HIS K 136 Details of bonding type rmsd covalent geometry : bond 0.00283 (16863) covalent geometry : angle 0.61649 (22683) hydrogen bonds : bond 0.03733 ( 696) hydrogen bonds : angle 4.86588 ( 1926) metal coordination : bond 0.00861 ( 16) metal coordination : angle 2.15943 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 216 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8201 (tttt) REVERT: A 288 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9085 (mp) REVERT: A 307 PHE cc_start: 0.7620 (m-80) cc_final: 0.7380 (m-80) REVERT: A 320 ASN cc_start: 0.8466 (t0) cc_final: 0.8192 (t0) REVERT: B 72 VAL cc_start: 0.8644 (t) cc_final: 0.8405 (p) REVERT: B 180 MET cc_start: 0.7197 (ppp) cc_final: 0.6715 (ppp) REVERT: B 181 MET cc_start: 0.8118 (tpp) cc_final: 0.7375 (mmm) REVERT: D 265 LEU cc_start: 0.8241 (tp) cc_final: 0.7951 (tp) REVERT: D 283 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8620 (tm-30) REVERT: D 295 THR cc_start: 0.8566 (p) cc_final: 0.8051 (t) REVERT: D 358 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.6902 (ptp) REVERT: E 177 TYR cc_start: 0.8401 (t80) cc_final: 0.8002 (t80) REVERT: E 180 MET cc_start: 0.7622 (mmp) cc_final: 0.7409 (mmp) REVERT: E 181 MET cc_start: 0.6105 (mpp) cc_final: 0.4694 (ttm) REVERT: G 271 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7491 (pm20) REVERT: G 305 ASP cc_start: 0.7957 (t0) cc_final: 0.7705 (t70) REVERT: I 64 GLN cc_start: 0.8068 (pm20) cc_final: 0.7580 (pm20) REVERT: J 264 THR cc_start: 0.8207 (m) cc_final: 0.7802 (p) REVERT: K 67 ASP cc_start: 0.7474 (p0) cc_final: 0.7121 (t70) REVERT: K 103 TRP cc_start: 0.8073 (t60) cc_final: 0.7233 (t60) REVERT: K 132 GLU cc_start: 0.8627 (mm-30) cc_final: 0.7909 (mt-10) REVERT: K 155 LYS cc_start: 0.8071 (mppt) cc_final: 0.7613 (mmmt) REVERT: L 37 LYS cc_start: 0.5749 (mmtp) cc_final: 0.5488 (mmtm) REVERT: L 41 MET cc_start: 0.6014 (ppp) cc_final: 0.5734 (ppp) REVERT: L 43 TRP cc_start: 0.7668 (m-90) cc_final: 0.7102 (m-90) outliers start: 43 outliers final: 25 residues processed: 246 average time/residue: 0.1225 time to fit residues: 47.5095 Evaluate side-chains 238 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain E residue 36 TYR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 150 TYR Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain J residue 186 THR Chi-restraints excluded: chain J residue 249 ILE Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain L residue 40 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 74 optimal weight: 0.0970 chunk 67 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 155 optimal weight: 0.0050 chunk 86 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 138 optimal weight: 0.0570 chunk 168 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.6314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.131457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.094921 restraints weight = 45117.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.096496 restraints weight = 26300.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.095724 restraints weight = 19781.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.096444 restraints weight = 20701.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.096815 restraints weight = 17858.937| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16879 Z= 0.111 Angle : 0.619 11.860 22695 Z= 0.314 Chirality : 0.048 0.223 2537 Planarity : 0.003 0.045 2890 Dihedral : 4.721 53.388 2274 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.73 % Favored : 97.08 % Rotamer: Outliers : 1.85 % Allowed : 20.47 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.19), residues: 2018 helix: 1.26 (0.21), residues: 587 sheet: -0.40 (0.20), residues: 573 loop : -0.40 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 159 TYR 0.014 0.001 TYR J 308 PHE 0.014 0.001 PHE J 252 TRP 0.011 0.001 TRP E 74 HIS 0.005 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00255 (16863) covalent geometry : angle 0.61793 (22683) hydrogen bonds : bond 0.03550 ( 696) hydrogen bonds : angle 4.79851 ( 1926) metal coordination : bond 0.00849 ( 16) metal coordination : angle 1.85480 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8550 (ttmt) cc_final: 0.8240 (tttt) REVERT: A 307 PHE cc_start: 0.7628 (m-80) cc_final: 0.7393 (m-80) REVERT: A 320 ASN cc_start: 0.8458 (t0) cc_final: 0.8165 (t0) REVERT: B 72 VAL cc_start: 0.8617 (t) cc_final: 0.8373 (p) REVERT: D 265 LEU cc_start: 0.8210 (tp) cc_final: 0.7902 (tp) REVERT: D 283 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8680 (tm-30) REVERT: D 295 THR cc_start: 0.8551 (p) cc_final: 0.8034 (t) REVERT: E 177 TYR cc_start: 0.8410 (t80) cc_final: 0.8059 (t80) REVERT: E 181 MET cc_start: 0.6074 (mpp) cc_final: 0.4695 (ttm) REVERT: G 243 GLN cc_start: 0.8008 (mm-40) cc_final: 0.6928 (pm20) REVERT: G 271 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7512 (pm20) REVERT: G 305 ASP cc_start: 0.7959 (t0) cc_final: 0.7718 (t70) REVERT: H 121 MET cc_start: 0.8108 (mmm) cc_final: 0.7861 (mmt) REVERT: I 41 MET cc_start: 0.8630 (mmm) cc_final: 0.8428 (mmp) REVERT: I 64 GLN cc_start: 0.8036 (pm20) cc_final: 0.7528 (pm20) REVERT: J 264 THR cc_start: 0.8209 (m) cc_final: 0.7755 (p) REVERT: K 103 TRP cc_start: 0.8056 (t60) cc_final: 0.7259 (t60) REVERT: K 132 GLU cc_start: 0.8649 (mm-30) cc_final: 0.7856 (mt-10) REVERT: K 155 LYS cc_start: 0.8078 (mppt) cc_final: 0.7632 (mmmt) REVERT: L 37 LYS cc_start: 0.5756 (mmtp) cc_final: 0.5531 (mmtm) REVERT: L 41 MET cc_start: 0.6111 (ppp) cc_final: 0.5862 (ppp) REVERT: L 43 TRP cc_start: 0.7667 (m-90) cc_final: 0.7097 (m-90) outliers start: 33 outliers final: 23 residues processed: 235 average time/residue: 0.1183 time to fit residues: 44.1446 Evaluate side-chains 230 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain E residue 36 TYR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 118 HIS Chi-restraints excluded: chain H residue 127 TYR Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain J residue 249 ILE Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain L residue 40 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 23 optimal weight: 30.0000 chunk 107 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 chunk 58 optimal weight: 0.2980 chunk 65 optimal weight: 0.2980 chunk 112 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.130765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.100067 restraints weight = 45117.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.098407 restraints weight = 30759.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.099371 restraints weight = 30428.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.099924 restraints weight = 21749.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.100621 restraints weight = 19788.016| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16879 Z= 0.127 Angle : 0.633 11.520 22695 Z= 0.322 Chirality : 0.048 0.243 2537 Planarity : 0.003 0.043 2890 Dihedral : 4.776 53.077 2274 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.97 % Favored : 96.83 % Rotamer: Outliers : 1.68 % Allowed : 20.81 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.19), residues: 2018 helix: 1.22 (0.21), residues: 587 sheet: -0.44 (0.21), residues: 555 loop : -0.38 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 38 TYR 0.022 0.001 TYR H 127 PHE 0.014 0.001 PHE J 252 TRP 0.010 0.001 TRP J 234 HIS 0.005 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00298 (16863) covalent geometry : angle 0.63147 (22683) hydrogen bonds : bond 0.03735 ( 696) hydrogen bonds : angle 4.83451 ( 1926) metal coordination : bond 0.00693 ( 16) metal coordination : angle 1.82707 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.0522 (tpt) cc_final: -0.1559 (mtt) REVERT: A 73 MET cc_start: 0.6731 (mmt) cc_final: 0.6504 (mmt) REVERT: A 138 LYS cc_start: 0.8355 (ttmt) cc_final: 0.8099 (tttt) REVERT: A 288 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9057 (mp) REVERT: A 307 PHE cc_start: 0.7652 (m-80) cc_final: 0.7420 (m-80) REVERT: A 320 ASN cc_start: 0.8430 (t0) cc_final: 0.8127 (t0) REVERT: B 12 ILE cc_start: 0.8933 (mt) cc_final: 0.8707 (mt) REVERT: B 72 VAL cc_start: 0.8767 (t) cc_final: 0.8477 (p) REVERT: B 171 GLU cc_start: 0.8599 (pm20) cc_final: 0.8292 (pm20) REVERT: B 181 MET cc_start: 0.7721 (tpt) cc_final: 0.7012 (mmm) REVERT: D 265 LEU cc_start: 0.8103 (tp) cc_final: 0.7867 (tp) REVERT: D 283 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8596 (tm-30) REVERT: D 295 THR cc_start: 0.8581 (p) cc_final: 0.8064 (t) REVERT: D 358 MET cc_start: 0.7242 (ptp) cc_final: 0.6997 (ptp) REVERT: E 177 TYR cc_start: 0.8338 (t80) cc_final: 0.7947 (t80) REVERT: E 181 MET cc_start: 0.6060 (mpp) cc_final: 0.4383 (ttm) REVERT: G 243 GLN cc_start: 0.7921 (mm-40) cc_final: 0.6935 (pm20) REVERT: G 271 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7428 (pm20) REVERT: I 41 MET cc_start: 0.8638 (mmm) cc_final: 0.8435 (mmp) REVERT: I 64 GLN cc_start: 0.8011 (pm20) cc_final: 0.7578 (pm20) REVERT: J 247 MET cc_start: 0.4791 (ppp) cc_final: 0.4371 (ppp) REVERT: J 264 THR cc_start: 0.8020 (m) cc_final: 0.7617 (p) REVERT: K 103 TRP cc_start: 0.8037 (t60) cc_final: 0.7249 (t60) REVERT: K 155 LYS cc_start: 0.7927 (mppt) cc_final: 0.7480 (mmmt) REVERT: L 37 LYS cc_start: 0.5920 (mmtp) cc_final: 0.5636 (mmtm) REVERT: L 41 MET cc_start: 0.6055 (ppp) cc_final: 0.5725 (ppp) REVERT: L 43 TRP cc_start: 0.7365 (m-90) cc_final: 0.7008 (m-90) outliers start: 30 outliers final: 21 residues processed: 237 average time/residue: 0.1145 time to fit residues: 43.0958 Evaluate side-chains 229 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain E residue 36 TYR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 118 HIS Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain J residue 249 ILE Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain L residue 40 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 198 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 171 optimal weight: 0.0060 chunk 78 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 163 optimal weight: 0.4980 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.130353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.099146 restraints weight = 45003.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.097349 restraints weight = 30809.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.098181 restraints weight = 31424.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.098884 restraints weight = 22359.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.099598 restraints weight = 20086.711| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16879 Z= 0.125 Angle : 0.620 11.348 22695 Z= 0.317 Chirality : 0.048 0.245 2537 Planarity : 0.003 0.041 2890 Dihedral : 4.763 53.249 2274 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.02 % Favored : 96.78 % Rotamer: Outliers : 1.85 % Allowed : 20.92 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.19), residues: 2018 helix: 1.20 (0.21), residues: 587 sheet: -0.45 (0.21), residues: 555 loop : -0.36 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 38 TYR 0.017 0.001 TYR G 341 PHE 0.014 0.001 PHE J 252 TRP 0.009 0.001 TRP J 234 HIS 0.006 0.001 HIS B 136 Details of bonding type rmsd covalent geometry : bond 0.00293 (16863) covalent geometry : angle 0.61891 (22683) hydrogen bonds : bond 0.03695 ( 696) hydrogen bonds : angle 4.82898 ( 1926) metal coordination : bond 0.00640 ( 16) metal coordination : angle 1.76247 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2989.27 seconds wall clock time: 52 minutes 27.36 seconds (3147.36 seconds total)