Starting phenix.real_space_refine on Tue May 27 04:50:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c5z_16445/05_2025/8c5z_16445.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c5z_16445/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8c5z_16445/05_2025/8c5z_16445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c5z_16445/05_2025/8c5z_16445.map" model { file = "/net/cci-nas-00/data/ceres_data/8c5z_16445/05_2025/8c5z_16445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c5z_16445/05_2025/8c5z_16445.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.45, per 1000 atoms: 0.57 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: 4.25 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.36 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: 5.05 Time building geometry restraints manager: 4.95 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: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 41.670 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.630 ------------------------------------------------------------------------------- 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 : 12.18 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (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 TRP 0.032 0.002 TRP K 122 HIS 0.005 0.001 HIS D 239 PHE 0.021 0.002 PHE J 252 TYR 0.020 0.002 TYR H 127 ARG 0.007 0.000 ARG B 4 Details of bonding type rmsd hydrogen bonds : bond 0.14482 ( 696) hydrogen bonds : angle 6.84204 ( 1926) metal coordination : bond 0.02122 ( 16) metal coordination : angle 2.94002 ( 12) covalent geometry : bond 0.00393 (16863) covalent geometry : angle 0.70158 (22683) *********************** 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 : 1.885 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: symmetry clash revert: symmetry clash REVERT: A 126 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8468 (tm-30) REVERT: A 128 TYR cc_start: 0.8420 (t80) cc_final: 0.8163 (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: 0.8660 (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: 0.7730 (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: 0.3774 (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: 0.9086 (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: 0.7480 (p0) REVERT: K 112 GLU cc_start: 0.7713 (tp30) cc_final: 0.7361 (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: 0.8284 (pp) REVERT: L 97 LEU cc_start: 0.8943 (tt) cc_final: 0.8468 (tt) outliers start: 3 outliers final: 2 residues processed: 385 average time/residue: 0.3380 time to fit residues: 181.6479 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 : 1.941 ------------------------------------------------------------------------------- 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 170 optimal weight: 9.9990 chunk 153 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 52 optimal weight: 0.3980 chunk 103 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN K 149 GLN ** L 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.132757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.091887 restraints weight = 45382.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.094582 restraints weight = 25521.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.096280 restraints weight = 18680.780| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2001 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= 0.136 Angle : 0.655 8.600 22695 Z= 0.345 Chirality : 0.049 0.194 2537 Planarity : 0.004 0.049 2890 Dihedral : 5.120 53.672 2276 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.17 % Favored : 96.63 % Rotamer: Outliers : 1.34 % Allowed : 11.35 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.18), residues: 2018 helix: 0.76 (0.20), residues: 616 sheet: -0.40 (0.20), residues: 573 loop : -0.59 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 122 HIS 0.009 0.002 HIS C 80 PHE 0.022 0.002 PHE A 326 TYR 0.018 0.002 TYR J 308 ARG 0.005 0.000 ARG A 325 Details of bonding type rmsd hydrogen bonds : bond 0.04512 ( 696) hydrogen bonds : angle 5.54546 ( 1926) metal coordination : bond 0.01513 ( 16) metal coordination : angle 2.72339 ( 12) covalent geometry : bond 0.00302 (16863) covalent geometry : angle 0.65241 (22683) *********************** 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 280 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 256 time to evaluate : 2.029 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: 0.8841 (mt-10) cc_final: 0.8403 (tm-30) REVERT: A 128 TYR cc_start: 0.8085 (t80) cc_final: 0.7858 (t80) REVERT: A 320 ASN cc_start: 0.8423 (t0) cc_final: 0.8094 (t0) REVERT: C 20 ARG cc_start: 0.7786 (mtp-110) cc_final: 0.7209 (ttt180) REVERT: C 41 MET cc_start: 0.5813 (tmm) cc_final: 0.5469 (tmm) REVERT: C 42 PHE cc_start: 0.7804 (p90) cc_final: 0.7333 (p90) REVERT: C 58 ASP cc_start: 0.7507 (t0) cc_final: 0.6692 (m-30) REVERT: D 265 LEU cc_start: 0.8243 (tp) cc_final: 0.7985 (tp) REVERT: D 295 THR cc_start: 0.8368 (p) cc_final: 0.7834 (t) REVERT: E 177 TYR cc_start: 0.8251 (t80) cc_final: 0.8032 (t80) REVERT: E 181 MET cc_start: 0.6169 (mpp) cc_final: 0.4952 (ttm) REVERT: H 121 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7571 (mmt) REVERT: H 150 TYR cc_start: 0.7664 (m-10) cc_final: 0.6695 (m-10) REVERT: J 223 LYS cc_start: 0.7162 (tptp) cc_final: 0.6916 (mmtt) REVERT: J 265 LEU cc_start: 0.7323 (tp) cc_final: 0.7110 (tt) REVERT: J 358 MET cc_start: 0.3522 (mpp) cc_final: 0.3158 (mpp) REVERT: K 132 GLU cc_start: 0.8526 (mm-30) cc_final: 0.7964 (mt-10) REVERT: K 155 LYS cc_start: 0.8166 (mppt) cc_final: 0.7805 (mmmt) REVERT: L 43 TRP cc_start: 0.7696 (m-90) cc_final: 0.6823 (m-90) REVERT: L 82 TYR cc_start: 0.6968 (t80) cc_final: 0.6660 (m-10) outliers start: 24 outliers final: 14 residues processed: 271 average time/residue: 0.3054 time to fit residues: 121.3260 Evaluate side-chains 217 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 1.891 ------------------------------------------------------------------------------- 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 157 LYS 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 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 50 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 191 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 199 optimal weight: 8.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN ** 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 = 0.4134 r_free = 0.4134 target = 0.131637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.093636 restraints weight = 44795.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.094868 restraints weight = 28603.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.095123 restraints weight = 20492.322| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16879 Z= 0.133 Angle : 0.611 8.487 22695 Z= 0.319 Chirality : 0.048 0.157 2537 Planarity : 0.004 0.045 2890 Dihedral : 4.947 49.381 2274 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.87 % Favored : 96.93 % Rotamer: Outliers : 1.85 % Allowed : 14.09 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.18), residues: 2018 helix: 0.81 (0.20), residues: 616 sheet: -0.41 (0.20), residues: 576 loop : -0.63 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP I 117 HIS 0.006 0.001 HIS K 136 PHE 0.017 0.001 PHE J 252 TYR 0.017 0.001 TYR J 308 ARG 0.005 0.000 ARG I 71 Details of bonding type rmsd hydrogen bonds : bond 0.04184 ( 696) hydrogen bonds : angle 5.23282 ( 1926) metal coordination : bond 0.01294 ( 16) metal coordination : angle 2.46142 ( 12) covalent geometry : bond 0.00305 (16863) covalent geometry : angle 0.60824 (22683) *********************** 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 270 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8429 (tptt) cc_final: 0.8189 (ttpt) REVERT: A 138 LYS cc_start: 0.8530 (ttmt) cc_final: 0.8229 (ttpt) REVERT: C 36 ASP cc_start: 0.7459 (m-30) cc_final: 0.6729 (p0) REVERT: C 41 MET cc_start: 0.5980 (tmm) cc_final: 0.5532 (tmm) REVERT: C 42 PHE cc_start: 0.8120 (p90) cc_final: 0.7592 (p90) REVERT: C 58 ASP cc_start: 0.7781 (t0) cc_final: 0.7527 (t0) REVERT: D 265 LEU cc_start: 0.8211 (tp) cc_final: 0.7940 (tp) REVERT: D 295 THR cc_start: 0.8379 (p) cc_final: 0.7847 (t) REVERT: E 177 TYR cc_start: 0.8417 (t80) cc_final: 0.8070 (t80) REVERT: E 181 MET cc_start: 0.6165 (mpp) cc_final: 0.4988 (ttm) REVERT: F 39 ASP cc_start: 0.8674 (t0) cc_final: 0.8204 (p0) REVERT: G 271 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7426 (pm20) REVERT: H 149 GLN cc_start: 0.8572 (pt0) cc_final: 0.8282 (pt0) REVERT: K 103 TRP cc_start: 0.8146 (t60) cc_final: 0.7353 (t60) REVERT: K 155 LYS cc_start: 0.8164 (mppt) cc_final: 0.7796 (mmmt) REVERT: L 43 TRP cc_start: 0.7632 (m-90) cc_final: 0.6808 (m-90) outliers start: 33 outliers final: 19 residues processed: 257 average time/residue: 0.2796 time to fit residues: 108.5386 Evaluate side-chains 231 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 2.144 ------------------------------------------------------------------------------- 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 97 ILE Chi-restraints excluded: chain E residue 105 ASP 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 F residue 111 LEU Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain H residue 127 TYR Chi-restraints excluded: chain J residue 186 THR Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 80 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 55 optimal weight: 7.9990 chunk 193 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.129392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.091225 restraints weight = 44847.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.092461 restraints weight = 28579.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.092485 restraints weight = 20911.646| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16879 Z= 0.187 Angle : 0.642 9.020 22695 Z= 0.335 Chirality : 0.049 0.235 2537 Planarity : 0.004 0.043 2890 Dihedral : 4.990 47.919 2274 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.37 % Favored : 96.43 % Rotamer: Outliers : 2.24 % Allowed : 16.95 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.18), residues: 2018 helix: 0.84 (0.20), residues: 616 sheet: -0.51 (0.21), residues: 543 loop : -0.67 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 117 HIS 0.006 0.001 HIS B 136 PHE 0.016 0.002 PHE J 252 TYR 0.014 0.002 TYR J 308 ARG 0.012 0.001 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 696) hydrogen bonds : angle 5.28632 ( 1926) metal coordination : bond 0.00800 ( 16) metal coordination : angle 2.50360 ( 12) covalent geometry : bond 0.00444 (16863) covalent geometry : angle 0.63952 (22683) *********************** 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 262 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 222 time to evaluate : 1.877 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: 0.8481 (t0) cc_final: 0.8261 (t0) REVERT: B 121 MET cc_start: 0.8015 (tpp) cc_final: 0.7529 (tpp) REVERT: C 41 MET cc_start: 0.6015 (tmm) cc_final: 0.5721 (tmm) REVERT: C 58 ASP cc_start: 0.7884 (t0) cc_final: 0.7633 (t0) REVERT: D 265 LEU cc_start: 0.8248 (tp) cc_final: 0.7999 (tp) REVERT: D 295 THR cc_start: 0.8474 (p) cc_final: 0.7936 (t) REVERT: E 177 TYR cc_start: 0.8419 (t80) cc_final: 0.8103 (t80) REVERT: E 181 MET cc_start: 0.6344 (mpp) cc_final: 0.5183 (ttm) REVERT: G 271 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7430 (pm20) REVERT: G 305 ASP cc_start: 0.8152 (t0) cc_final: 0.7822 (t70) REVERT: G 358 MET cc_start: 0.8130 (mmp) cc_final: 0.7875 (mmp) REVERT: H 58 ASP cc_start: 0.6734 (p0) cc_final: 0.6492 (p0) REVERT: I 117 TRP cc_start: 0.6076 (p90) cc_final: 0.5426 (p-90) REVERT: J 247 MET cc_start: 0.5421 (tmm) cc_final: 0.5119 (ppp) REVERT: K 132 GLU cc_start: 0.8643 (mm-30) cc_final: 0.7914 (mt-10) REVERT: K 155 LYS cc_start: 0.8162 (mppt) cc_final: 0.7725 (mmmt) REVERT: L 43 TRP cc_start: 0.7621 (m-90) cc_final: 0.6956 (m-90) outliers start: 40 outliers final: 24 residues processed: 246 average time/residue: 0.2671 time to fit residues: 100.5811 Evaluate side-chains 223 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 283 GLU 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 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 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 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 127 TYR Chi-restraints excluded: chain J residue 186 THR Chi-restraints excluded: chain L residue 52 ILE 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 126 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 193 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 146 optimal weight: 6.9990 chunk 16 optimal weight: 0.0370 chunk 176 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 162 ASN ** 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 = 0.4140 r_free = 0.4140 target = 0.131194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.100661 restraints weight = 45225.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.098552 restraints weight = 31236.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.099815 restraints weight = 30758.049| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3170 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= 0.119 Angle : 0.590 9.193 22695 Z= 0.308 Chirality : 0.047 0.169 2537 Planarity : 0.004 0.063 2890 Dihedral : 4.812 48.293 2274 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.73 % Favored : 97.08 % Rotamer: Outliers : 2.18 % Allowed : 18.57 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.18), residues: 2018 helix: 0.91 (0.21), residues: 619 sheet: -0.45 (0.21), residues: 573 loop : -0.64 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP I 117 HIS 0.005 0.001 HIS K 136 PHE 0.014 0.001 PHE I 42 TYR 0.016 0.001 TYR J 308 ARG 0.008 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 696) hydrogen bonds : angle 5.02344 ( 1926) metal coordination : bond 0.01136 ( 16) metal coordination : angle 2.21711 ( 12) covalent geometry : bond 0.00273 (16863) covalent geometry : angle 0.58773 (22683) *********************** 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 274 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 235 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ASN cc_start: 0.8415 (t0) cc_final: 0.8154 (t0) REVERT: B 121 MET cc_start: 0.7826 (tpp) cc_final: 0.7321 (tpp) REVERT: B 180 MET cc_start: 0.7357 (ppp) cc_final: 0.7118 (ppp) REVERT: C 41 MET cc_start: 0.6052 (tmm) cc_final: 0.5771 (tmm) REVERT: C 58 ASP cc_start: 0.7712 (t0) cc_final: 0.7471 (t0) REVERT: D 265 LEU cc_start: 0.8152 (tp) cc_final: 0.7905 (tp) REVERT: D 295 THR cc_start: 0.8468 (p) cc_final: 0.7914 (t) REVERT: E 177 TYR cc_start: 0.8384 (t80) cc_final: 0.7948 (t80) REVERT: E 181 MET cc_start: 0.6289 (mpp) cc_final: 0.4777 (ttm) REVERT: F 105 ARG cc_start: 0.8465 (mtm110) cc_final: 0.8239 (mtm110) REVERT: G 271 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7372 (pm20) REVERT: G 305 ASP cc_start: 0.8035 (t0) cc_final: 0.7833 (t70) REVERT: H 58 ASP cc_start: 0.6762 (p0) cc_final: 0.6510 (p0) REVERT: H 127 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.7924 (m-10) REVERT: J 247 MET cc_start: 0.5254 (tmm) cc_final: 0.5017 (ppp) REVERT: J 264 THR cc_start: 0.7933 (m) cc_final: 0.7592 (p) REVERT: K 103 TRP cc_start: 0.8030 (t60) cc_final: 0.7300 (t60) REVERT: K 155 LYS cc_start: 0.7901 (mppt) cc_final: 0.7493 (mmmt) REVERT: L 43 TRP cc_start: 0.7283 (m-90) cc_final: 0.6860 (m-90) REVERT: L 80 HIS cc_start: 0.6935 (OUTLIER) cc_final: 0.6101 (m-70) outliers start: 39 outliers final: 19 residues processed: 262 average time/residue: 0.2722 time to fit residues: 109.1501 Evaluate side-chains 230 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 283 GLU 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 C residue 65 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 36 TYR 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 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 50 optimal weight: 0.0060 chunk 21 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 0.0870 chunk 184 optimal weight: 0.8980 chunk 157 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.5774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 162 ASN ** 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 = 0.4148 r_free = 0.4148 target = 0.131814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.096783 restraints weight = 45115.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.096298 restraints weight = 28195.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.096703 restraints weight = 21866.926| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16879 Z= 0.109 Angle : 0.602 16.616 22695 Z= 0.309 Chirality : 0.048 0.205 2537 Planarity : 0.003 0.047 2890 Dihedral : 4.767 50.513 2274 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.82 % Favored : 96.98 % Rotamer: Outliers : 2.24 % Allowed : 18.79 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.19), residues: 2018 helix: 1.28 (0.21), residues: 587 sheet: -0.39 (0.20), residues: 573 loop : -0.41 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 43 HIS 0.005 0.001 HIS K 136 PHE 0.025 0.001 PHE C 42 TYR 0.018 0.001 TYR J 308 ARG 0.007 0.000 ARG E 79 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 696) hydrogen bonds : angle 4.88253 ( 1926) metal coordination : bond 0.01194 ( 16) metal coordination : angle 2.11412 ( 12) covalent geometry : bond 0.00248 (16863) covalent geometry : angle 0.60065 (22683) *********************** 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 270 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 230 time to evaluate : 1.943 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 138 LYS cc_start: 0.8537 (ttmt) cc_final: 0.8161 (tttt) REVERT: A 320 ASN cc_start: 0.8411 (t0) cc_final: 0.8154 (t0) REVERT: B 121 MET cc_start: 0.7799 (tpp) cc_final: 0.7364 (tpp) REVERT: C 36 ASP cc_start: 0.7027 (m-30) cc_final: 0.6504 (p0) REVERT: C 41 MET cc_start: 0.6012 (tmm) cc_final: 0.5702 (tmm) REVERT: C 58 ASP cc_start: 0.7661 (t0) cc_final: 0.7399 (t0) REVERT: D 265 LEU cc_start: 0.8258 (tp) cc_final: 0.7968 (tp) REVERT: D 295 THR cc_start: 0.8486 (p) cc_final: 0.7946 (t) REVERT: E 177 TYR cc_start: 0.8452 (t80) cc_final: 0.8006 (t80) REVERT: E 181 MET cc_start: 0.6303 (mpp) cc_final: 0.4820 (ttm) REVERT: F 105 ARG cc_start: 0.8573 (mtm110) cc_final: 0.8272 (mtm110) REVERT: G 271 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7407 (pm20) REVERT: H 58 ASP cc_start: 0.6717 (p0) cc_final: 0.6416 (p0) REVERT: I 117 TRP cc_start: 0.5737 (p-90) cc_final: 0.5474 (p-90) REVERT: J 247 MET cc_start: 0.5334 (tmm) cc_final: 0.5054 (ppp) REVERT: J 264 THR cc_start: 0.8112 (m) cc_final: 0.7697 (p) REVERT: K 103 TRP cc_start: 0.8069 (t60) cc_final: 0.7355 (t60) REVERT: K 132 GLU cc_start: 0.8610 (mm-30) cc_final: 0.7874 (mt-10) REVERT: K 155 LYS cc_start: 0.8030 (mppt) cc_final: 0.7602 (mmmt) REVERT: L 43 TRP cc_start: 0.7527 (m-90) cc_final: 0.7008 (m-90) REVERT: L 80 HIS cc_start: 0.7254 (OUTLIER) cc_final: 0.6513 (m-70) outliers start: 40 outliers final: 19 residues processed: 257 average time/residue: 0.2617 time to fit residues: 103.2399 Evaluate side-chains 228 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 314 GLU 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 248 THR 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 65 VAL 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 170 LEU 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 177 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 182 optimal weight: 0.0050 chunk 147 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 157 optimal weight: 8.9990 chunk 109 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 overall best weight: 1.6198 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.129938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.099274 restraints weight = 44981.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.097454 restraints weight = 32262.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.098570 restraints weight = 31754.828| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16879 Z= 0.151 Angle : 0.620 12.508 22695 Z= 0.320 Chirality : 0.048 0.195 2537 Planarity : 0.004 0.043 2890 Dihedral : 4.876 54.182 2274 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.32 % Favored : 96.48 % Rotamer: Outliers : 2.52 % Allowed : 19.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.18), residues: 2018 helix: 1.05 (0.21), residues: 619 sheet: -0.48 (0.20), residues: 565 loop : -0.68 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 43 HIS 0.005 0.001 HIS B 136 PHE 0.013 0.002 PHE J 252 TYR 0.011 0.001 TYR C 40 ARG 0.006 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.03955 ( 696) hydrogen bonds : angle 4.94874 ( 1926) metal coordination : bond 0.00777 ( 16) metal coordination : angle 2.18602 ( 12) covalent geometry : bond 0.00360 (16863) covalent geometry : angle 0.61845 (22683) *********************** 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 259 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 214 time to evaluate : 1.962 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: A 87 LYS cc_start: 0.8416 (tttt) cc_final: 0.7912 (ttmt) REVERT: A 138 LYS cc_start: 0.8411 (ttmt) cc_final: 0.8069 (tttt) REVERT: A 320 ASN cc_start: 0.8477 (t0) cc_final: 0.8199 (t0) REVERT: B 121 MET cc_start: 0.7835 (tpp) cc_final: 0.7342 (tpp) REVERT: B 180 MET cc_start: 0.7180 (ppp) cc_final: 0.6834 (ppp) REVERT: C 36 ASP cc_start: 0.7042 (m-30) cc_final: 0.6456 (p0) REVERT: C 41 MET cc_start: 0.6232 (tmm) cc_final: 0.5931 (tmm) REVERT: C 58 ASP cc_start: 0.7787 (t0) cc_final: 0.7541 (t0) REVERT: D 265 LEU cc_start: 0.8187 (tp) cc_final: 0.7932 (tp) REVERT: D 295 THR cc_start: 0.8549 (p) cc_final: 0.8031 (t) REVERT: E 177 TYR cc_start: 0.8485 (t80) cc_final: 0.7989 (t80) REVERT: E 181 MET cc_start: 0.6454 (mpp) cc_final: 0.4892 (ttm) REVERT: F 105 ARG cc_start: 0.8481 (mtm110) cc_final: 0.8210 (mtm110) REVERT: G 271 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7488 (pm20) REVERT: J 264 THR cc_start: 0.8015 (m) cc_final: 0.7656 (p) REVERT: K 155 LYS cc_start: 0.7991 (mppt) cc_final: 0.7532 (mmmt) REVERT: L 37 LYS cc_start: 0.5750 (mmtp) cc_final: 0.5365 (mmtm) REVERT: L 43 TRP cc_start: 0.7502 (m-90) cc_final: 0.7241 (m-90) REVERT: L 80 HIS cc_start: 0.7188 (OUTLIER) cc_final: 0.6214 (m-70) outliers start: 45 outliers final: 27 residues processed: 246 average time/residue: 0.2595 time to fit residues: 97.9457 Evaluate side-chains 231 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 1.862 ------------------------------------------------------------------------------- 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 358 MET Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 36 TYR Chi-restraints excluded: chain E residue 45 ILE 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 69 ILE 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 K residue 46 VAL Chi-restraints excluded: chain L residue 40 TYR Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 80 HIS Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 12 optimal weight: 10.0000 chunk 183 optimal weight: 0.1980 chunk 85 optimal weight: 0.9980 chunk 124 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 157 optimal weight: 8.9990 chunk 137 optimal weight: 0.0040 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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 = 0.4147 r_free = 0.4147 target = 0.131888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.094792 restraints weight = 44721.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.096451 restraints weight = 26376.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.096047 restraints weight = 19106.874| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 16879 Z= 0.111 Angle : 0.619 12.165 22695 Z= 0.316 Chirality : 0.048 0.182 2537 Planarity : 0.003 0.046 2890 Dihedral : 4.765 54.104 2274 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.68 % Favored : 97.13 % Rotamer: Outliers : 1.73 % Allowed : 20.36 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.19), residues: 2018 helix: 1.28 (0.21), residues: 587 sheet: -0.39 (0.21), residues: 573 loop : -0.38 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 74 HIS 0.005 0.001 HIS K 125 PHE 0.016 0.001 PHE C 42 TYR 0.017 0.001 TYR A 341 ARG 0.005 0.000 ARG E 79 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 696) hydrogen bonds : angle 4.83658 ( 1926) metal coordination : bond 0.01084 ( 16) metal coordination : angle 1.94965 ( 12) covalent geometry : bond 0.00248 (16863) covalent geometry : angle 0.61709 (22683) *********************** 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 262 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 1.956 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: 0.8524 (ttmt) cc_final: 0.8179 (tttt) REVERT: A 216 ASP cc_start: 0.7531 (p0) cc_final: 0.7261 (p0) REVERT: A 320 ASN cc_start: 0.8454 (t0) cc_final: 0.8151 (t0) REVERT: B 180 MET cc_start: 0.7221 (ppp) cc_final: 0.6966 (ppp) REVERT: C 43 TRP cc_start: 0.7406 (m-90) cc_final: 0.6991 (m-90) REVERT: C 58 ASP cc_start: 0.7718 (t0) cc_final: 0.6854 (m-30) REVERT: D 265 LEU cc_start: 0.8251 (tp) cc_final: 0.7936 (tp) REVERT: D 295 THR cc_start: 0.8530 (p) cc_final: 0.8006 (t) REVERT: D 358 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.6940 (ptp) REVERT: E 177 TYR cc_start: 0.8471 (t80) cc_final: 0.7974 (t80) REVERT: E 181 MET cc_start: 0.6403 (mpp) cc_final: 0.4837 (ttm) REVERT: F 105 ARG cc_start: 0.8603 (mtm110) cc_final: 0.8277 (ttm110) REVERT: G 271 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7510 (pm20) REVERT: I 64 GLN cc_start: 0.8109 (pm20) cc_final: 0.7650 (pm20) REVERT: J 264 THR cc_start: 0.8215 (m) cc_final: 0.7769 (p) REVERT: K 67 ASP cc_start: 0.7589 (p0) cc_final: 0.7099 (t70) REVERT: K 132 GLU cc_start: 0.8596 (mm-30) cc_final: 0.7841 (mt-10) REVERT: K 155 LYS cc_start: 0.8065 (mppt) cc_final: 0.7631 (mmmt) REVERT: L 37 LYS cc_start: 0.5824 (mmtp) cc_final: 0.5516 (mmtm) REVERT: L 43 TRP cc_start: 0.7610 (m-90) cc_final: 0.7277 (m-90) REVERT: L 80 HIS cc_start: 0.7320 (OUTLIER) cc_final: 0.6573 (m-70) outliers start: 31 outliers final: 14 residues processed: 253 average time/residue: 0.2706 time to fit residues: 104.6672 Evaluate side-chains 217 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 2.073 ------------------------------------------------------------------------------- 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 85 VAL Chi-restraints excluded: chain C residue 111 LEU 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 F residue 38 MET 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 97 ILE Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain J residue 186 THR Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain L residue 40 TYR Chi-restraints excluded: chain L residue 80 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 164 optimal weight: 7.9990 chunk 94 optimal weight: 0.5980 chunk 196 optimal weight: 0.0970 chunk 154 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.131622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.094872 restraints weight = 45576.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.095756 restraints weight = 28098.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.096330 restraints weight = 19629.446| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3885 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= 0.116 Angle : 0.635 12.519 22695 Z= 0.322 Chirality : 0.048 0.208 2537 Planarity : 0.003 0.045 2890 Dihedral : 4.735 53.963 2274 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.12 % Favored : 96.68 % Rotamer: Outliers : 1.62 % Allowed : 21.20 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.19), residues: 2018 helix: 1.27 (0.21), residues: 587 sheet: -0.38 (0.21), residues: 570 loop : -0.41 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 234 HIS 0.005 0.001 HIS B 136 PHE 0.017 0.001 PHE C 42 TYR 0.017 0.001 TYR K 61 ARG 0.012 0.000 ARG I 7 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 696) hydrogen bonds : angle 4.82550 ( 1926) metal coordination : bond 0.00866 ( 16) metal coordination : angle 1.98548 ( 12) covalent geometry : bond 0.00267 (16863) covalent geometry : angle 0.63323 (22683) *********************** 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 238 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 2.059 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 73 MET cc_start: 0.6706 (mmt) cc_final: 0.6471 (mmt) REVERT: A 79 ASN cc_start: 0.8416 (t0) cc_final: 0.8190 (t0) REVERT: A 138 LYS cc_start: 0.8495 (ttmt) cc_final: 0.8187 (tttt) REVERT: A 216 ASP cc_start: 0.7413 (p0) cc_final: 0.7156 (p0) REVERT: A 320 ASN cc_start: 0.8427 (t0) cc_final: 0.8153 (t0) REVERT: D 265 LEU cc_start: 0.8225 (tp) cc_final: 0.7918 (tp) REVERT: D 295 THR cc_start: 0.8545 (p) cc_final: 0.8028 (t) REVERT: D 301 LYS cc_start: 0.9032 (tptm) cc_final: 0.8764 (tptp) REVERT: D 358 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.7104 (ptp) REVERT: E 177 TYR cc_start: 0.8448 (t80) cc_final: 0.7980 (t80) REVERT: E 181 MET cc_start: 0.6360 (mpp) cc_final: 0.4746 (ttm) REVERT: F 105 ARG cc_start: 0.8511 (mtm110) cc_final: 0.8221 (mtm110) REVERT: G 243 GLN cc_start: 0.7977 (mm-40) cc_final: 0.6919 (pm20) REVERT: G 271 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7514 (pm20) REVERT: I 41 MET cc_start: 0.8610 (mmm) cc_final: 0.8397 (mmp) REVERT: J 264 THR cc_start: 0.8126 (m) cc_final: 0.7708 (p) REVERT: K 103 TRP cc_start: 0.8108 (t60) cc_final: 0.7226 (t60) REVERT: K 132 GLU cc_start: 0.8598 (mm-30) cc_final: 0.7821 (mt-10) REVERT: K 155 LYS cc_start: 0.8019 (mppt) cc_final: 0.7577 (mmmt) REVERT: L 37 LYS cc_start: 0.5837 (mmtp) cc_final: 0.5561 (mmtm) REVERT: L 43 TRP cc_start: 0.7513 (m-90) cc_final: 0.7240 (m-90) REVERT: L 80 HIS cc_start: 0.7214 (OUTLIER) cc_final: 0.6408 (m-70) outliers start: 29 outliers final: 17 residues processed: 227 average time/residue: 0.2692 time to fit residues: 94.9354 Evaluate side-chains 220 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 2.194 ------------------------------------------------------------------------------- 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 85 VAL Chi-restraints excluded: chain C residue 111 LEU 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 105 ASP Chi-restraints excluded: chain E residue 153 THR 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 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 339 VAL Chi-restraints excluded: chain L residue 40 TYR Chi-restraints excluded: chain L residue 80 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 191 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 193 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 64 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.128232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.085737 restraints weight = 45347.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.088343 restraints weight = 26477.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.089847 restraints weight = 19517.605| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 16879 Z= 0.225 Angle : 0.713 11.347 22695 Z= 0.368 Chirality : 0.050 0.212 2537 Planarity : 0.004 0.037 2890 Dihedral : 5.173 56.058 2274 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.01 % Favored : 95.79 % Rotamer: Outliers : 1.57 % Allowed : 21.42 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.18), residues: 2018 helix: 0.84 (0.21), residues: 619 sheet: -0.56 (0.22), residues: 501 loop : -0.78 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 43 HIS 0.006 0.002 HIS B 136 PHE 0.022 0.002 PHE A 307 TYR 0.025 0.002 TYR H 127 ARG 0.010 0.001 ARG I 7 Details of bonding type rmsd hydrogen bonds : bond 0.04616 ( 696) hydrogen bonds : angle 5.19026 ( 1926) metal coordination : bond 0.01004 ( 16) metal coordination : angle 2.13188 ( 12) covalent geometry : bond 0.00539 (16863) covalent geometry : angle 0.71194 (22683) ********************** 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 224 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8604 (ttmt) cc_final: 0.8294 (tttt) REVERT: A 216 ASP cc_start: 0.7746 (p0) cc_final: 0.7521 (p0) REVERT: C 58 ASP cc_start: 0.7705 (t0) cc_final: 0.7277 (m-30) REVERT: D 265 LEU cc_start: 0.8259 (tp) cc_final: 0.7963 (tp) REVERT: D 295 THR cc_start: 0.8678 (p) cc_final: 0.8246 (t) REVERT: D 358 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7251 (ptp) REVERT: E 177 TYR cc_start: 0.8487 (t80) cc_final: 0.8001 (t80) REVERT: E 181 MET cc_start: 0.6676 (mpp) cc_final: 0.5089 (ttm) REVERT: G 243 GLN cc_start: 0.8071 (mm-40) cc_final: 0.6997 (pm20) REVERT: G 271 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: J 264 THR cc_start: 0.8144 (m) cc_final: 0.7741 (p) REVERT: J 300 ARG cc_start: 0.8575 (ttm170) cc_final: 0.8249 (ttp-170) REVERT: L 37 LYS cc_start: 0.5880 (mmtp) cc_final: 0.5570 (mmtm) REVERT: L 43 TRP cc_start: 0.7709 (m-90) cc_final: 0.7144 (m-90) REVERT: L 80 HIS cc_start: 0.7367 (OUTLIER) cc_final: 0.6780 (m-70) outliers start: 28 outliers final: 18 residues processed: 215 average time/residue: 0.2550 time to fit residues: 85.6029 Evaluate side-chains 210 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain C residue 111 LEU 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 F residue 69 ILE Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain J residue 247 MET Chi-restraints excluded: chain J residue 249 ILE Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 80 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 41 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 198 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 26 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.130170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.089746 restraints weight = 45055.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.092480 restraints weight = 25398.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.094215 restraints weight = 18574.700| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16879 Z= 0.127 Angle : 0.661 11.509 22695 Z= 0.337 Chirality : 0.048 0.208 2537 Planarity : 0.003 0.041 2890 Dihedral : 4.986 55.547 2274 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.73 % Favored : 97.08 % Rotamer: Outliers : 1.45 % Allowed : 21.98 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.18), residues: 2018 helix: 0.85 (0.21), residues: 619 sheet: -0.58 (0.21), residues: 552 loop : -0.69 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 43 HIS 0.006 0.001 HIS K 136 PHE 0.015 0.001 PHE C 42 TYR 0.018 0.001 TYR G 341 ARG 0.010 0.000 ARG I 7 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 696) hydrogen bonds : angle 5.01009 ( 1926) metal coordination : bond 0.00761 ( 16) metal coordination : angle 1.89515 ( 12) covalent geometry : bond 0.00296 (16863) covalent geometry : angle 0.65965 (22683) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5428.22 seconds wall clock time: 95 minutes 50.09 seconds (5750.09 seconds total)