Starting phenix.real_space_refine on Tue Nov 18 14:59:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5vms_8712/11_2025/5vms_8712.cif Found real_map, /net/cci-nas-00/data/ceres_data/5vms_8712/11_2025/5vms_8712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5vms_8712/11_2025/5vms_8712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5vms_8712/11_2025/5vms_8712.map" model { file = "/net/cci-nas-00/data/ceres_data/5vms_8712/11_2025/5vms_8712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5vms_8712/11_2025/5vms_8712.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 12 9.91 5 S 64 5.16 5 C 9708 2.51 5 N 2588 2.21 5 O 2544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14916 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2717 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 7, 'TRANS': 335} Chain breaks: 2 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 4, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1009 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 138} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 79 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 14, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: C, E, G, D, F, H Residues with excluded nonbonded symmetry interactions: 4 residue: pdb="CA CA B 202 " occ=0.83 residue: pdb="CA CA D 202 " occ=0.83 residue: pdb="CA CA F 202 " occ=0.83 residue: pdb="CA CA H 202 " occ=0.83 Time building chain proxies: 2.78, per 1000 atoms: 0.19 Number of scatterers: 14916 At special positions: 0 Unit cell: (107.9, 107.9, 123.5, 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) Ca 12 19.99 S 64 16.00 O 2544 8.00 N 2588 7.00 C 9708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 681.9 milliseconds 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3600 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 0 sheets defined 82.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 109 through 135 Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 139 through 168 removed outlier: 4.795A pdb=" N GLU A 144 " --> pdb=" O ASN A 140 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL A 152 " --> pdb=" O TRP A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.509A pdb=" N ARG A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 206 Processing helix chain 'A' and resid 218 through 228 removed outlier: 4.245A pdb=" N PHE A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 removed outlier: 3.532A pdb=" N ASP A 232 " --> pdb=" O LEU A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 235 through 248 removed outlier: 4.161A pdb=" N LEU A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 274 removed outlier: 3.553A pdb=" N THR A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 312 through 350 removed outlier: 4.131A pdb=" N VAL A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE A 325 " --> pdb=" O CYS A 321 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 356 through 376 removed outlier: 4.582A pdb=" N ALA A 360 " --> pdb=" O ARG A 356 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU A 375 " --> pdb=" O CYS A 371 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 523 Processing helix chain 'A' and resid 526 through 556 Processing helix chain 'B' and resid 7 through 22 removed outlier: 4.180A pdb=" N LYS B 22 " --> pdb=" O SER B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 41 removed outlier: 3.536A pdb=" N LEU B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 57 removed outlier: 3.538A pdb=" N VAL B 56 " --> pdb=" O MET B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 75 Processing helix chain 'B' and resid 79 through 94 removed outlier: 3.651A pdb=" N GLU B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 138 through 146 Processing helix chain 'C' and resid 95 through 105 Processing helix chain 'C' and resid 109 through 135 Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 139 through 168 removed outlier: 4.795A pdb=" N GLU C 144 " --> pdb=" O ASN C 140 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR C 145 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 151 " --> pdb=" O PHE C 147 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL C 152 " --> pdb=" O TRP C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 175 through 186 removed outlier: 3.509A pdb=" N ARG C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS C 186 " --> pdb=" O ARG C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 206 Processing helix chain 'C' and resid 218 through 228 removed outlier: 4.245A pdb=" N PHE C 222 " --> pdb=" O ARG C 218 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET C 228 " --> pdb=" O GLN C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 232 removed outlier: 3.532A pdb=" N ASP C 232 " --> pdb=" O LEU C 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 229 through 232' Processing helix chain 'C' and resid 235 through 248 removed outlier: 4.161A pdb=" N LEU C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU C 241 " --> pdb=" O THR C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 274 removed outlier: 3.553A pdb=" N THR C 254 " --> pdb=" O GLN C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 302 Processing helix chain 'C' and resid 312 through 350 removed outlier: 4.131A pdb=" N VAL C 324 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE C 325 " --> pdb=" O CYS C 321 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA C 326 " --> pdb=" O PHE C 322 " (cutoff:3.500A) Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 353 through 355 No H-bonds generated for 'chain 'C' and resid 353 through 355' Processing helix chain 'C' and resid 356 through 376 removed outlier: 4.582A pdb=" N ALA C 360 " --> pdb=" O ARG C 356 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU C 375 " --> pdb=" O CYS C 371 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN C 376 " --> pdb=" O TYR C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 523 Processing helix chain 'C' and resid 526 through 556 Processing helix chain 'D' and resid 7 through 22 removed outlier: 4.180A pdb=" N LYS D 22 " --> pdb=" O SER D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 41 removed outlier: 3.536A pdb=" N LEU D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 57 removed outlier: 3.538A pdb=" N VAL D 56 " --> pdb=" O MET D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 75 Processing helix chain 'D' and resid 79 through 94 removed outlier: 3.651A pdb=" N GLU D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 113 Processing helix chain 'D' and resid 118 through 130 Processing helix chain 'D' and resid 138 through 146 Processing helix chain 'E' and resid 95 through 105 Processing helix chain 'E' and resid 109 through 135 Processing helix chain 'E' and resid 136 through 138 No H-bonds generated for 'chain 'E' and resid 136 through 138' Processing helix chain 'E' and resid 139 through 168 removed outlier: 4.795A pdb=" N GLU E 144 " --> pdb=" O ASN E 140 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR E 145 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE E 151 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL E 152 " --> pdb=" O TRP E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 171 No H-bonds generated for 'chain 'E' and resid 169 through 171' Processing helix chain 'E' and resid 175 through 186 removed outlier: 3.509A pdb=" N ARG E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 206 Processing helix chain 'E' and resid 218 through 228 removed outlier: 4.245A pdb=" N PHE E 222 " --> pdb=" O ARG E 218 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET E 228 " --> pdb=" O GLN E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 232 removed outlier: 3.532A pdb=" N ASP E 232 " --> pdb=" O LEU E 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 229 through 232' Processing helix chain 'E' and resid 235 through 248 removed outlier: 4.161A pdb=" N LEU E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU E 241 " --> pdb=" O THR E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 274 removed outlier: 3.553A pdb=" N THR E 254 " --> pdb=" O GLN E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 302 Processing helix chain 'E' and resid 312 through 350 removed outlier: 4.131A pdb=" N VAL E 324 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE E 325 " --> pdb=" O CYS E 321 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA E 326 " --> pdb=" O PHE E 322 " (cutoff:3.500A) Proline residue: E 333 - end of helix Processing helix chain 'E' and resid 353 through 355 No H-bonds generated for 'chain 'E' and resid 353 through 355' Processing helix chain 'E' and resid 356 through 376 removed outlier: 4.582A pdb=" N ALA E 360 " --> pdb=" O ARG E 356 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU E 375 " --> pdb=" O CYS E 371 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN E 376 " --> pdb=" O TYR E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 523 Processing helix chain 'E' and resid 526 through 556 Processing helix chain 'F' and resid 7 through 22 removed outlier: 4.180A pdb=" N LYS F 22 " --> pdb=" O SER F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 41 removed outlier: 3.536A pdb=" N LEU F 33 " --> pdb=" O THR F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 57 removed outlier: 3.538A pdb=" N VAL F 56 " --> pdb=" O MET F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 75 Processing helix chain 'F' and resid 79 through 94 removed outlier: 3.651A pdb=" N GLU F 85 " --> pdb=" O ASP F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 113 Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 138 through 146 Processing helix chain 'G' and resid 95 through 105 Processing helix chain 'G' and resid 109 through 135 Processing helix chain 'G' and resid 136 through 138 No H-bonds generated for 'chain 'G' and resid 136 through 138' Processing helix chain 'G' and resid 139 through 168 removed outlier: 4.795A pdb=" N GLU G 144 " --> pdb=" O ASN G 140 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR G 145 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE G 151 " --> pdb=" O PHE G 147 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL G 152 " --> pdb=" O TRP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 171 No H-bonds generated for 'chain 'G' and resid 169 through 171' Processing helix chain 'G' and resid 175 through 186 removed outlier: 3.509A pdb=" N ARG G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS G 186 " --> pdb=" O ARG G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 206 Processing helix chain 'G' and resid 218 through 228 removed outlier: 4.245A pdb=" N PHE G 222 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET G 228 " --> pdb=" O GLN G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 232 removed outlier: 3.532A pdb=" N ASP G 232 " --> pdb=" O LEU G 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 229 through 232' Processing helix chain 'G' and resid 235 through 248 removed outlier: 4.161A pdb=" N LEU G 240 " --> pdb=" O GLY G 236 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU G 241 " --> pdb=" O THR G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 274 removed outlier: 3.553A pdb=" N THR G 254 " --> pdb=" O GLN G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 302 Processing helix chain 'G' and resid 312 through 350 removed outlier: 4.131A pdb=" N VAL G 324 " --> pdb=" O SER G 320 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE G 325 " --> pdb=" O CYS G 321 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA G 326 " --> pdb=" O PHE G 322 " (cutoff:3.500A) Proline residue: G 333 - end of helix Processing helix chain 'G' and resid 353 through 355 No H-bonds generated for 'chain 'G' and resid 353 through 355' Processing helix chain 'G' and resid 356 through 376 removed outlier: 4.582A pdb=" N ALA G 360 " --> pdb=" O ARG G 356 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU G 375 " --> pdb=" O CYS G 371 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN G 376 " --> pdb=" O TYR G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 523 Processing helix chain 'G' and resid 526 through 556 Processing helix chain 'H' and resid 7 through 22 removed outlier: 4.180A pdb=" N LYS H 22 " --> pdb=" O SER H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 41 removed outlier: 3.536A pdb=" N LEU H 33 " --> pdb=" O THR H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 57 removed outlier: 3.538A pdb=" N VAL H 56 " --> pdb=" O MET H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 75 Processing helix chain 'H' and resid 79 through 94 removed outlier: 3.651A pdb=" N GLU H 85 " --> pdb=" O ASP H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 113 Processing helix chain 'H' and resid 118 through 130 Processing helix chain 'H' and resid 138 through 146 1112 hydrogen bonds defined for protein. 3336 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2476 1.33 - 1.45: 4192 1.45 - 1.57: 8440 1.57 - 1.69: 8 1.69 - 1.81: 112 Bond restraints: 15228 Sorted by residual: bond pdb=" C LEU E 332 " pdb=" O LEU E 332 " ideal model delta sigma weight residual 1.241 1.212 0.029 9.80e-03 1.04e+04 8.83e+00 bond pdb=" C LEU A 332 " pdb=" O LEU A 332 " ideal model delta sigma weight residual 1.241 1.212 0.029 9.80e-03 1.04e+04 8.83e+00 bond pdb=" C LEU C 332 " pdb=" O LEU C 332 " ideal model delta sigma weight residual 1.241 1.212 0.029 9.80e-03 1.04e+04 8.83e+00 bond pdb=" C LEU G 332 " pdb=" O LEU G 332 " ideal model delta sigma weight residual 1.241 1.212 0.029 9.80e-03 1.04e+04 8.83e+00 bond pdb=" C ILE C 264 " pdb=" O ILE C 264 " ideal model delta sigma weight residual 1.237 1.270 -0.033 1.13e-02 7.83e+03 8.52e+00 ... (remaining 15223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 13828 1.37 - 2.73: 5568 2.73 - 4.10: 1080 4.10 - 5.47: 124 5.47 - 6.83: 44 Bond angle restraints: 20644 Sorted by residual: angle pdb=" N ILE E 303 " pdb=" CA ILE E 303 " pdb=" C ILE E 303 " ideal model delta sigma weight residual 110.74 104.41 6.33 9.10e-01 1.21e+00 4.84e+01 angle pdb=" N ILE G 303 " pdb=" CA ILE G 303 " pdb=" C ILE G 303 " ideal model delta sigma weight residual 110.74 104.41 6.33 9.10e-01 1.21e+00 4.84e+01 angle pdb=" N ILE C 303 " pdb=" CA ILE C 303 " pdb=" C ILE C 303 " ideal model delta sigma weight residual 110.74 104.41 6.33 9.10e-01 1.21e+00 4.84e+01 angle pdb=" N ILE A 303 " pdb=" CA ILE A 303 " pdb=" C ILE A 303 " ideal model delta sigma weight residual 110.74 104.41 6.33 9.10e-01 1.21e+00 4.84e+01 angle pdb=" N ASP F 21 " pdb=" CA ASP F 21 " pdb=" C ASP F 21 " ideal model delta sigma weight residual 111.33 117.80 -6.47 1.21e+00 6.83e-01 2.86e+01 ... (remaining 20639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.79: 7524 12.79 - 25.59: 1012 25.59 - 38.38: 228 38.38 - 51.17: 64 51.17 - 63.96: 20 Dihedral angle restraints: 8848 sinusoidal: 3260 harmonic: 5588 Sorted by residual: dihedral pdb=" CA SER C 323 " pdb=" C SER C 323 " pdb=" N VAL C 324 " pdb=" CA VAL C 324 " ideal model delta harmonic sigma weight residual -180.00 -155.83 -24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA SER A 323 " pdb=" C SER A 323 " pdb=" N VAL A 324 " pdb=" CA VAL A 324 " ideal model delta harmonic sigma weight residual -180.00 -155.83 -24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA SER G 323 " pdb=" C SER G 323 " pdb=" N VAL G 324 " pdb=" CA VAL G 324 " ideal model delta harmonic sigma weight residual -180.00 -155.83 -24.17 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 8845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1764 0.071 - 0.143: 440 0.143 - 0.214: 128 0.214 - 0.285: 28 0.285 - 0.357: 8 Chirality restraints: 2368 Sorted by residual: chirality pdb=" CA LEU G 332 " pdb=" N LEU G 332 " pdb=" C LEU G 332 " pdb=" CB LEU G 332 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CA LEU A 332 " pdb=" N LEU A 332 " pdb=" C LEU A 332 " pdb=" CB LEU A 332 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CA LEU C 332 " pdb=" N LEU C 332 " pdb=" C LEU C 332 " pdb=" CB LEU C 332 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 2365 not shown) Planarity restraints: 2576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 66 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO B 67 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 67 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 67 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 66 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO H 67 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO H 67 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 67 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 66 " -0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO D 67 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " -0.035 5.00e-02 4.00e+02 ... (remaining 2573 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 560 2.77 - 3.30: 17496 3.30 - 3.83: 25306 3.83 - 4.37: 26534 4.37 - 4.90: 43930 Nonbonded interactions: 113826 Sorted by model distance: nonbonded pdb=" O THR F 63 " pdb="CA CA F 202 " model vdw 2.234 2.510 nonbonded pdb=" O THR H 63 " pdb="CA CA H 202 " model vdw 2.234 2.510 nonbonded pdb=" O THR B 63 " pdb="CA CA B 202 " model vdw 2.234 2.510 nonbonded pdb=" O THR D 63 " pdb="CA CA D 202 " model vdw 2.234 2.510 nonbonded pdb=" OE1 GLN E 549 " pdb=" CD1 LEU G 548 " model vdw 2.236 3.460 ... (remaining 113821 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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=0.83 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.070 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 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 : 0.007 0.043 15228 Z= 0.532 Angle : 1.474 6.833 20644 Z= 1.155 Chirality : 0.074 0.357 2368 Planarity : 0.005 0.063 2576 Dihedral : 12.688 63.961 5248 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.16), residues: 1904 helix: 2.39 (0.10), residues: 1472 sheet: None (None), residues: 0 loop : -2.54 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 106 TYR 0.016 0.002 TYR G 534 PHE 0.019 0.002 PHE G 330 TRP 0.028 0.002 TRP C 369 HIS 0.005 0.001 HIS E 116 Details of bonding type rmsd covalent geometry : bond 0.00738 (15228) covalent geometry : angle 1.47399 (20644) hydrogen bonds : bond 0.11619 ( 1112) hydrogen bonds : angle 4.38215 ( 3336) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 896 time to evaluate : 0.598 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: A 141 LEU cc_start: 0.8035 (tp) cc_final: 0.7812 (tt) REVERT: A 153 LEU cc_start: 0.9398 (tp) cc_final: 0.9176 (tp) REVERT: A 160 GLU cc_start: 0.9549 (tt0) cc_final: 0.9214 (tt0) REVERT: A 180 ARG cc_start: 0.8066 (mtt180) cc_final: 0.7702 (mmt-90) REVERT: A 225 ILE cc_start: 0.9442 (mt) cc_final: 0.9222 (mt) REVERT: A 291 ASP cc_start: 0.8333 (m-30) cc_final: 0.8113 (m-30) REVERT: A 308 LYS cc_start: 0.8849 (mttt) cc_final: 0.8608 (mmtp) REVERT: A 358 ILE cc_start: 0.8879 (mt) cc_final: 0.8571 (mt) REVERT: A 499 HIS cc_start: 0.7998 (m-70) cc_final: 0.7671 (p90) REVERT: A 526 ASP cc_start: 0.8839 (t70) cc_final: 0.8448 (t70) REVERT: A 534 TYR cc_start: 0.8879 (t80) cc_final: 0.7769 (t80) REVERT: A 551 ARG cc_start: 0.8707 (tpp-160) cc_final: 0.8396 (tpt90) REVERT: B 37 MET cc_start: 0.9455 (mmm) cc_final: 0.9206 (mmm) REVERT: B 39 SER cc_start: 0.9561 (t) cc_final: 0.9307 (p) REVERT: B 45 THR cc_start: 0.8969 (m) cc_final: 0.8663 (t) REVERT: B 52 MET cc_start: 0.9423 (mtm) cc_final: 0.9002 (mtp) REVERT: B 80 THR cc_start: 0.8229 (p) cc_final: 0.8011 (p) REVERT: B 93 PHE cc_start: 0.8231 (m-80) cc_final: 0.7882 (m-80) REVERT: B 125 MET cc_start: 0.9466 (ttt) cc_final: 0.9245 (ttp) REVERT: B 142 PHE cc_start: 0.8570 (t80) cc_final: 0.8329 (t80) REVERT: C 141 LEU cc_start: 0.8035 (tp) cc_final: 0.7813 (tt) REVERT: C 153 LEU cc_start: 0.9400 (tp) cc_final: 0.9177 (tp) REVERT: C 160 GLU cc_start: 0.9549 (tt0) cc_final: 0.9214 (tt0) REVERT: C 180 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7703 (mmt-90) REVERT: C 225 ILE cc_start: 0.9441 (mt) cc_final: 0.9222 (mt) REVERT: C 291 ASP cc_start: 0.8333 (m-30) cc_final: 0.8113 (m-30) REVERT: C 308 LYS cc_start: 0.8847 (mttt) cc_final: 0.8607 (mmtp) REVERT: C 358 ILE cc_start: 0.8878 (mt) cc_final: 0.8570 (mt) REVERT: C 499 HIS cc_start: 0.7998 (m-70) cc_final: 0.7670 (p90) REVERT: C 526 ASP cc_start: 0.8837 (t70) cc_final: 0.8446 (t70) REVERT: C 534 TYR cc_start: 0.8878 (t80) cc_final: 0.7768 (t80) REVERT: C 550 ARG cc_start: 0.9169 (ttm110) cc_final: 0.8959 (mtp-110) REVERT: D 37 MET cc_start: 0.9454 (mmm) cc_final: 0.9206 (mmm) REVERT: D 39 SER cc_start: 0.9561 (t) cc_final: 0.9306 (p) REVERT: D 45 THR cc_start: 0.8971 (m) cc_final: 0.8665 (t) REVERT: D 52 MET cc_start: 0.9423 (mtm) cc_final: 0.9001 (mtp) REVERT: D 80 THR cc_start: 0.8229 (p) cc_final: 0.8013 (p) REVERT: D 93 PHE cc_start: 0.8230 (m-80) cc_final: 0.7880 (m-80) REVERT: D 125 MET cc_start: 0.9466 (ttt) cc_final: 0.9244 (ttp) REVERT: D 142 PHE cc_start: 0.8568 (t80) cc_final: 0.8328 (t80) REVERT: E 141 LEU cc_start: 0.8034 (tp) cc_final: 0.7811 (tt) REVERT: E 153 LEU cc_start: 0.9399 (tp) cc_final: 0.9177 (tp) REVERT: E 160 GLU cc_start: 0.9550 (tt0) cc_final: 0.9214 (tt0) REVERT: E 180 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7703 (mmt-90) REVERT: E 225 ILE cc_start: 0.9440 (mt) cc_final: 0.9221 (mt) REVERT: E 291 ASP cc_start: 0.8333 (m-30) cc_final: 0.8114 (m-30) REVERT: E 308 LYS cc_start: 0.8848 (mttt) cc_final: 0.8606 (mmtp) REVERT: E 358 ILE cc_start: 0.8877 (mt) cc_final: 0.8569 (mt) REVERT: E 499 HIS cc_start: 0.7999 (m-70) cc_final: 0.7671 (p90) REVERT: E 526 ASP cc_start: 0.8838 (t70) cc_final: 0.8446 (t70) REVERT: E 534 TYR cc_start: 0.8876 (t80) cc_final: 0.7768 (t80) REVERT: E 550 ARG cc_start: 0.9169 (ttm110) cc_final: 0.8960 (mtp-110) REVERT: F 37 MET cc_start: 0.9455 (mmm) cc_final: 0.9207 (mmm) REVERT: F 39 SER cc_start: 0.9560 (t) cc_final: 0.9306 (p) REVERT: F 45 THR cc_start: 0.8970 (m) cc_final: 0.8663 (t) REVERT: F 52 MET cc_start: 0.9423 (mtm) cc_final: 0.9001 (mtp) REVERT: F 80 THR cc_start: 0.8228 (p) cc_final: 0.8010 (p) REVERT: F 93 PHE cc_start: 0.8230 (m-80) cc_final: 0.7879 (m-80) REVERT: F 125 MET cc_start: 0.9466 (ttt) cc_final: 0.9244 (ttp) REVERT: F 142 PHE cc_start: 0.8569 (t80) cc_final: 0.8329 (t80) REVERT: G 141 LEU cc_start: 0.8034 (tp) cc_final: 0.7812 (tt) REVERT: G 153 LEU cc_start: 0.9398 (tp) cc_final: 0.9175 (tp) REVERT: G 160 GLU cc_start: 0.9550 (tt0) cc_final: 0.9214 (tt0) REVERT: G 180 ARG cc_start: 0.8067 (mtt180) cc_final: 0.7702 (mmt-90) REVERT: G 225 ILE cc_start: 0.9441 (mt) cc_final: 0.9222 (mt) REVERT: G 291 ASP cc_start: 0.8332 (m-30) cc_final: 0.8113 (m-30) REVERT: G 308 LYS cc_start: 0.8849 (mttt) cc_final: 0.8609 (mmtp) REVERT: G 358 ILE cc_start: 0.8878 (mt) cc_final: 0.8570 (mt) REVERT: G 499 HIS cc_start: 0.8000 (m-70) cc_final: 0.7672 (p90) REVERT: G 526 ASP cc_start: 0.8838 (t70) cc_final: 0.8447 (t70) REVERT: G 534 TYR cc_start: 0.8877 (t80) cc_final: 0.7767 (t80) REVERT: H 37 MET cc_start: 0.9456 (mmm) cc_final: 0.9206 (mmm) REVERT: H 39 SER cc_start: 0.9561 (t) cc_final: 0.9306 (p) REVERT: H 45 THR cc_start: 0.8970 (m) cc_final: 0.8665 (t) REVERT: H 52 MET cc_start: 0.9424 (mtm) cc_final: 0.9003 (mtp) REVERT: H 80 THR cc_start: 0.8228 (p) cc_final: 0.8010 (p) REVERT: H 93 PHE cc_start: 0.8231 (m-80) cc_final: 0.7881 (m-80) REVERT: H 125 MET cc_start: 0.9466 (ttt) cc_final: 0.9245 (ttp) REVERT: H 142 PHE cc_start: 0.8569 (t80) cc_final: 0.8328 (t80) outliers start: 0 outliers final: 0 residues processed: 896 average time/residue: 0.1178 time to fit residues: 156.7942 Evaluate side-chains 692 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 692 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN C 357 GLN ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN E 357 GLN ** E 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN G 357 GLN ** G 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.093428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.076369 restraints weight = 37122.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.079253 restraints weight = 18922.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.081319 restraints weight = 11878.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.082798 restraints weight = 8394.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.083762 restraints weight = 6425.131| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15228 Z= 0.153 Angle : 0.602 6.376 20644 Z= 0.325 Chirality : 0.041 0.221 2368 Planarity : 0.004 0.040 2576 Dihedral : 3.962 22.415 2104 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.83 % Allowed : 18.02 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.05 (0.19), residues: 1904 helix: 3.75 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.73 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 75 TYR 0.018 0.002 TYR C 534 PHE 0.026 0.002 PHE D 17 TRP 0.013 0.001 TRP A 166 HIS 0.006 0.001 HIS F 108 Details of bonding type rmsd covalent geometry : bond 0.00336 (15228) covalent geometry : angle 0.60181 (20644) hydrogen bonds : bond 0.04263 ( 1112) hydrogen bonds : angle 3.96328 ( 3336) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 688 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.8526 (t60) cc_final: 0.8139 (t60) REVERT: A 180 ARG cc_start: 0.8332 (mtt180) cc_final: 0.7864 (mpt-90) REVERT: A 291 ASP cc_start: 0.8498 (m-30) cc_final: 0.8124 (m-30) REVERT: A 308 LYS cc_start: 0.9041 (mttt) cc_final: 0.8512 (mttm) REVERT: A 350 ARG cc_start: 0.8895 (ptt-90) cc_final: 0.8694 (ptt-90) REVERT: A 384 ILE cc_start: 0.8115 (mp) cc_final: 0.7868 (mt) REVERT: A 499 HIS cc_start: 0.8528 (m-70) cc_final: 0.7999 (p-80) REVERT: A 526 ASP cc_start: 0.8867 (t70) cc_final: 0.8183 (t70) REVERT: A 533 GLN cc_start: 0.9094 (tm-30) cc_final: 0.8825 (tm-30) REVERT: A 534 TYR cc_start: 0.9088 (t80) cc_final: 0.8546 (t80) REVERT: A 536 GLN cc_start: 0.9554 (tt0) cc_final: 0.9327 (tt0) REVERT: A 551 ARG cc_start: 0.8868 (tpp-160) cc_final: 0.8493 (tpt170) REVERT: B 9 GLN cc_start: 0.8844 (mp10) cc_final: 0.8377 (pt0) REVERT: B 10 ILE cc_start: 0.8996 (tt) cc_final: 0.8770 (mt) REVERT: B 52 MET cc_start: 0.9167 (mtm) cc_final: 0.8910 (mtp) REVERT: B 72 MET cc_start: 0.9416 (ptm) cc_final: 0.9211 (ptp) REVERT: B 91 ARG cc_start: 0.8814 (ttm170) cc_final: 0.8609 (ttm110) REVERT: B 117 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8720 (mt) REVERT: B 121 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8280 (mm-30) REVERT: B 125 MET cc_start: 0.9482 (ttt) cc_final: 0.9242 (ttp) REVERT: B 142 PHE cc_start: 0.8955 (t80) cc_final: 0.8743 (t80) REVERT: C 166 TRP cc_start: 0.8525 (t60) cc_final: 0.8137 (t60) REVERT: C 180 ARG cc_start: 0.8329 (mtt180) cc_final: 0.7864 (mpt-90) REVERT: C 291 ASP cc_start: 0.8507 (m-30) cc_final: 0.8130 (m-30) REVERT: C 308 LYS cc_start: 0.9042 (mttt) cc_final: 0.8517 (mttm) REVERT: C 384 ILE cc_start: 0.8121 (mp) cc_final: 0.7878 (mt) REVERT: C 499 HIS cc_start: 0.8525 (m-70) cc_final: 0.7996 (p-80) REVERT: C 526 ASP cc_start: 0.8866 (t70) cc_final: 0.8180 (t70) REVERT: C 533 GLN cc_start: 0.9094 (tm-30) cc_final: 0.8827 (tm-30) REVERT: C 534 TYR cc_start: 0.9089 (t80) cc_final: 0.8546 (t80) REVERT: C 536 GLN cc_start: 0.9552 (tt0) cc_final: 0.9328 (tt0) REVERT: D 9 GLN cc_start: 0.8843 (mp10) cc_final: 0.8376 (pt0) REVERT: D 10 ILE cc_start: 0.8998 (tt) cc_final: 0.8772 (mt) REVERT: D 52 MET cc_start: 0.9169 (mtm) cc_final: 0.8909 (mtp) REVERT: D 72 MET cc_start: 0.9416 (ptm) cc_final: 0.9210 (ptp) REVERT: D 91 ARG cc_start: 0.8814 (ttm170) cc_final: 0.8609 (ttm110) REVERT: D 117 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8723 (mt) REVERT: D 121 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8277 (mm-30) REVERT: D 125 MET cc_start: 0.9480 (ttt) cc_final: 0.9243 (ttp) REVERT: D 142 PHE cc_start: 0.8952 (t80) cc_final: 0.8741 (t80) REVERT: E 166 TRP cc_start: 0.8536 (t60) cc_final: 0.8151 (t60) REVERT: E 180 ARG cc_start: 0.8331 (mtt180) cc_final: 0.7866 (mpt-90) REVERT: E 291 ASP cc_start: 0.8506 (m-30) cc_final: 0.8131 (m-30) REVERT: E 308 LYS cc_start: 0.9042 (mttt) cc_final: 0.8514 (mttm) REVERT: E 350 ARG cc_start: 0.8890 (ptt-90) cc_final: 0.8689 (ptt-90) REVERT: E 384 ILE cc_start: 0.8119 (mp) cc_final: 0.7876 (mt) REVERT: E 499 HIS cc_start: 0.8526 (m-70) cc_final: 0.7997 (p-80) REVERT: E 526 ASP cc_start: 0.8866 (t70) cc_final: 0.8181 (t70) REVERT: E 533 GLN cc_start: 0.9098 (tm-30) cc_final: 0.8828 (tm-30) REVERT: E 534 TYR cc_start: 0.9091 (t80) cc_final: 0.8545 (t80) REVERT: E 536 GLN cc_start: 0.9552 (tt0) cc_final: 0.9326 (tt0) REVERT: E 550 ARG cc_start: 0.9089 (ttm110) cc_final: 0.8872 (mtm110) REVERT: F 9 GLN cc_start: 0.8841 (mp10) cc_final: 0.8374 (pt0) REVERT: F 10 ILE cc_start: 0.9004 (tt) cc_final: 0.8775 (mt) REVERT: F 52 MET cc_start: 0.9164 (mtm) cc_final: 0.8910 (mtp) REVERT: F 72 MET cc_start: 0.9416 (ptm) cc_final: 0.9212 (ptp) REVERT: F 91 ARG cc_start: 0.8815 (ttm170) cc_final: 0.8611 (ttm110) REVERT: F 117 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8722 (mt) REVERT: F 121 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8273 (mm-30) REVERT: F 125 MET cc_start: 0.9484 (ttt) cc_final: 0.9240 (ttp) REVERT: F 142 PHE cc_start: 0.8949 (t80) cc_final: 0.8726 (t80) REVERT: G 166 TRP cc_start: 0.8528 (t60) cc_final: 0.8141 (t60) REVERT: G 180 ARG cc_start: 0.8327 (mtt180) cc_final: 0.7861 (mpt-90) REVERT: G 291 ASP cc_start: 0.8503 (m-30) cc_final: 0.8127 (m-30) REVERT: G 308 LYS cc_start: 0.9040 (mttt) cc_final: 0.8511 (mttm) REVERT: G 350 ARG cc_start: 0.8894 (ptt-90) cc_final: 0.8693 (ptt-90) REVERT: G 384 ILE cc_start: 0.8118 (mp) cc_final: 0.7871 (mt) REVERT: G 499 HIS cc_start: 0.8523 (m-70) cc_final: 0.7996 (p-80) REVERT: G 526 ASP cc_start: 0.8867 (t70) cc_final: 0.8183 (t70) REVERT: G 533 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8826 (tm-30) REVERT: G 534 TYR cc_start: 0.9089 (t80) cc_final: 0.8543 (t80) REVERT: G 536 GLN cc_start: 0.9555 (tt0) cc_final: 0.9328 (tt0) REVERT: G 548 LEU cc_start: 0.9426 (tp) cc_final: 0.9086 (tp) REVERT: G 549 GLN cc_start: 0.9386 (tp40) cc_final: 0.9031 (tp40) REVERT: H 9 GLN cc_start: 0.8841 (mp10) cc_final: 0.8374 (pt0) REVERT: H 10 ILE cc_start: 0.8997 (tt) cc_final: 0.8771 (mt) REVERT: H 52 MET cc_start: 0.9165 (mtm) cc_final: 0.8909 (mtp) REVERT: H 72 MET cc_start: 0.9415 (ptm) cc_final: 0.9211 (ptp) REVERT: H 91 ARG cc_start: 0.8816 (ttm170) cc_final: 0.8610 (ttm110) REVERT: H 117 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8720 (mt) REVERT: H 121 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8279 (mm-30) REVERT: H 125 MET cc_start: 0.9482 (ttt) cc_final: 0.9242 (ttp) REVERT: H 142 PHE cc_start: 0.8947 (t80) cc_final: 0.8736 (t80) outliers start: 70 outliers final: 51 residues processed: 710 average time/residue: 0.1069 time to fit residues: 116.2529 Evaluate side-chains 710 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 655 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 498 HIS Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 498 HIS Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 498 HIS Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 146 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 191 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN B 54 ASN B 112 ASN C 366 GLN D 54 ASN D 112 ASN E 366 GLN F 54 ASN F 112 ASN G 366 GLN H 54 ASN H 112 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.091798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.074788 restraints weight = 38472.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.077558 restraints weight = 19671.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.079539 restraints weight = 12472.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.080915 restraints weight = 8911.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.081736 restraints weight = 6932.183| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15228 Z= 0.168 Angle : 0.568 6.232 20644 Z= 0.305 Chirality : 0.040 0.157 2368 Planarity : 0.003 0.030 2576 Dihedral : 3.813 19.883 2104 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 7.18 % Allowed : 19.13 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.89 (0.20), residues: 1904 helix: 3.54 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.38 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 227 TYR 0.017 0.002 TYR E 268 PHE 0.019 0.002 PHE C 260 TRP 0.008 0.001 TRP E 110 HIS 0.005 0.001 HIS F 108 Details of bonding type rmsd covalent geometry : bond 0.00374 (15228) covalent geometry : angle 0.56830 (20644) hydrogen bonds : bond 0.03888 ( 1112) hydrogen bonds : angle 3.99524 ( 3336) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 649 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.8641 (t60) cc_final: 0.8223 (t60) REVERT: A 180 ARG cc_start: 0.8324 (mtt180) cc_final: 0.7887 (mpt-90) REVERT: A 291 ASP cc_start: 0.8383 (m-30) cc_final: 0.8066 (m-30) REVERT: A 307 ASP cc_start: 0.8908 (p0) cc_final: 0.8674 (p0) REVERT: A 308 LYS cc_start: 0.9082 (mttt) cc_final: 0.8649 (mttm) REVERT: A 350 ARG cc_start: 0.8809 (ptt-90) cc_final: 0.8595 (ptt-90) REVERT: A 355 ASN cc_start: 0.8298 (p0) cc_final: 0.7975 (p0) REVERT: A 384 ILE cc_start: 0.8058 (mp) cc_final: 0.7781 (mt) REVERT: A 499 HIS cc_start: 0.8475 (m-70) cc_final: 0.8020 (p-80) REVERT: A 526 ASP cc_start: 0.8897 (t70) cc_final: 0.8232 (t70) REVERT: A 536 GLN cc_start: 0.9588 (tt0) cc_final: 0.9281 (tt0) REVERT: B 9 GLN cc_start: 0.8814 (mp10) cc_final: 0.8316 (pt0) REVERT: B 37 MET cc_start: 0.9416 (mmm) cc_final: 0.9198 (mmm) REVERT: B 46 GLU cc_start: 0.9053 (tp30) cc_final: 0.8822 (tp30) REVERT: B 52 MET cc_start: 0.9192 (mtm) cc_final: 0.8841 (mtp) REVERT: B 54 ASN cc_start: 0.9159 (m-40) cc_final: 0.8867 (m110) REVERT: B 77 MET cc_start: 0.8414 (mmm) cc_final: 0.8086 (mmm) REVERT: B 91 ARG cc_start: 0.8796 (ttm170) cc_final: 0.8541 (ttm-80) REVERT: B 115 GLU cc_start: 0.8419 (mp0) cc_final: 0.8090 (mp0) REVERT: B 117 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8811 (mt) REVERT: B 119 ASP cc_start: 0.8967 (p0) cc_final: 0.8627 (p0) REVERT: B 120 GLU cc_start: 0.9043 (tp30) cc_final: 0.8636 (mm-30) REVERT: B 124 GLU cc_start: 0.9220 (tp30) cc_final: 0.8922 (tp30) REVERT: B 125 MET cc_start: 0.9486 (ttt) cc_final: 0.9174 (ttt) REVERT: C 166 TRP cc_start: 0.8644 (t60) cc_final: 0.8230 (t60) REVERT: C 180 ARG cc_start: 0.8328 (mtt180) cc_final: 0.7891 (mpt-90) REVERT: C 291 ASP cc_start: 0.8380 (m-30) cc_final: 0.8060 (m-30) REVERT: C 307 ASP cc_start: 0.8908 (p0) cc_final: 0.8677 (p0) REVERT: C 308 LYS cc_start: 0.9076 (mttt) cc_final: 0.8642 (mttm) REVERT: C 355 ASN cc_start: 0.8296 (p0) cc_final: 0.7998 (p0) REVERT: C 384 ILE cc_start: 0.8061 (mp) cc_final: 0.7783 (mt) REVERT: C 499 HIS cc_start: 0.8476 (m-70) cc_final: 0.8019 (p-80) REVERT: C 526 ASP cc_start: 0.8898 (t70) cc_final: 0.8233 (t70) REVERT: C 533 GLN cc_start: 0.9185 (tm-30) cc_final: 0.8623 (tm-30) REVERT: C 536 GLN cc_start: 0.9588 (tt0) cc_final: 0.9284 (tt0) REVERT: D 9 GLN cc_start: 0.8816 (mp10) cc_final: 0.8402 (pt0) REVERT: D 37 MET cc_start: 0.9417 (mmm) cc_final: 0.9200 (mmm) REVERT: D 46 GLU cc_start: 0.9055 (tp30) cc_final: 0.8825 (tp30) REVERT: D 52 MET cc_start: 0.9183 (mtm) cc_final: 0.8838 (mtp) REVERT: D 54 ASN cc_start: 0.9159 (m-40) cc_final: 0.8866 (m110) REVERT: D 77 MET cc_start: 0.8425 (mmm) cc_final: 0.8095 (mmm) REVERT: D 91 ARG cc_start: 0.8797 (ttm170) cc_final: 0.8545 (ttm-80) REVERT: D 115 GLU cc_start: 0.8417 (mp0) cc_final: 0.8088 (mp0) REVERT: D 117 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8809 (mt) REVERT: D 119 ASP cc_start: 0.8980 (p0) cc_final: 0.8639 (p0) REVERT: D 120 GLU cc_start: 0.9041 (tp30) cc_final: 0.8635 (mm-30) REVERT: D 124 GLU cc_start: 0.9218 (tp30) cc_final: 0.8923 (tp30) REVERT: D 125 MET cc_start: 0.9487 (ttt) cc_final: 0.9177 (ttt) REVERT: E 166 TRP cc_start: 0.8650 (t60) cc_final: 0.8233 (t60) REVERT: E 180 ARG cc_start: 0.8323 (mtt180) cc_final: 0.7888 (mpt-90) REVERT: E 291 ASP cc_start: 0.8388 (m-30) cc_final: 0.8071 (m-30) REVERT: E 307 ASP cc_start: 0.8917 (p0) cc_final: 0.8685 (p0) REVERT: E 308 LYS cc_start: 0.9084 (mttt) cc_final: 0.8652 (mttm) REVERT: E 350 ARG cc_start: 0.8814 (ptt-90) cc_final: 0.8599 (ptt-90) REVERT: E 355 ASN cc_start: 0.8304 (p0) cc_final: 0.7983 (p0) REVERT: E 384 ILE cc_start: 0.8061 (mp) cc_final: 0.7786 (mt) REVERT: E 499 HIS cc_start: 0.8474 (m-70) cc_final: 0.8020 (p-80) REVERT: E 526 ASP cc_start: 0.8897 (t70) cc_final: 0.8231 (t70) REVERT: E 533 GLN cc_start: 0.9185 (tm-30) cc_final: 0.8621 (tm-30) REVERT: E 536 GLN cc_start: 0.9586 (tt0) cc_final: 0.9282 (tt0) REVERT: E 550 ARG cc_start: 0.9058 (ttm110) cc_final: 0.8853 (mtm110) REVERT: F 9 GLN cc_start: 0.8812 (mp10) cc_final: 0.8401 (pt0) REVERT: F 37 MET cc_start: 0.9416 (mmm) cc_final: 0.9199 (mmm) REVERT: F 46 GLU cc_start: 0.9055 (tp30) cc_final: 0.8826 (tp30) REVERT: F 52 MET cc_start: 0.9180 (mtm) cc_final: 0.8838 (mtp) REVERT: F 54 ASN cc_start: 0.9162 (m-40) cc_final: 0.8872 (m110) REVERT: F 77 MET cc_start: 0.8423 (mmm) cc_final: 0.8095 (mmm) REVERT: F 91 ARG cc_start: 0.8798 (ttm170) cc_final: 0.8545 (ttm-80) REVERT: F 115 GLU cc_start: 0.8420 (mp0) cc_final: 0.8092 (mp0) REVERT: F 117 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8807 (mt) REVERT: F 119 ASP cc_start: 0.8980 (p0) cc_final: 0.8640 (p0) REVERT: F 120 GLU cc_start: 0.9039 (tp30) cc_final: 0.8633 (mm-30) REVERT: F 124 GLU cc_start: 0.9220 (tp30) cc_final: 0.8922 (tp30) REVERT: F 125 MET cc_start: 0.9485 (ttt) cc_final: 0.9178 (ttt) REVERT: G 166 TRP cc_start: 0.8647 (t60) cc_final: 0.8235 (t60) REVERT: G 180 ARG cc_start: 0.8331 (mtt180) cc_final: 0.7893 (mpt-90) REVERT: G 291 ASP cc_start: 0.8382 (m-30) cc_final: 0.8062 (m-30) REVERT: G 307 ASP cc_start: 0.8909 (p0) cc_final: 0.8676 (p0) REVERT: G 308 LYS cc_start: 0.9081 (mttt) cc_final: 0.8646 (mttm) REVERT: G 350 ARG cc_start: 0.8812 (ptt-90) cc_final: 0.8597 (ptt-90) REVERT: G 355 ASN cc_start: 0.8305 (p0) cc_final: 0.7984 (p0) REVERT: G 384 ILE cc_start: 0.8057 (mp) cc_final: 0.7782 (mt) REVERT: G 499 HIS cc_start: 0.8468 (m-70) cc_final: 0.8016 (p-80) REVERT: G 526 ASP cc_start: 0.8907 (t70) cc_final: 0.8237 (t70) REVERT: G 533 GLN cc_start: 0.9184 (tm-30) cc_final: 0.8621 (tm-30) REVERT: G 536 GLN cc_start: 0.9591 (tt0) cc_final: 0.9287 (tt0) REVERT: H 9 GLN cc_start: 0.8812 (mp10) cc_final: 0.8315 (pt0) REVERT: H 37 MET cc_start: 0.9418 (mmm) cc_final: 0.9202 (mmm) REVERT: H 46 GLU cc_start: 0.9054 (tp30) cc_final: 0.8823 (tp30) REVERT: H 52 MET cc_start: 0.9189 (mtm) cc_final: 0.8839 (mtp) REVERT: H 54 ASN cc_start: 0.9160 (m-40) cc_final: 0.8867 (m110) REVERT: H 77 MET cc_start: 0.8423 (mmm) cc_final: 0.8097 (mmm) REVERT: H 91 ARG cc_start: 0.8800 (ttm170) cc_final: 0.8544 (ttm-80) REVERT: H 115 GLU cc_start: 0.8423 (mp0) cc_final: 0.8095 (mp0) REVERT: H 117 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8808 (mt) REVERT: H 119 ASP cc_start: 0.8969 (p0) cc_final: 0.8628 (p0) REVERT: H 120 GLU cc_start: 0.9038 (tp30) cc_final: 0.8631 (mm-30) REVERT: H 124 GLU cc_start: 0.9219 (tp30) cc_final: 0.8922 (tp30) REVERT: H 125 MET cc_start: 0.9485 (ttt) cc_final: 0.9176 (ttt) outliers start: 104 outliers final: 84 residues processed: 674 average time/residue: 0.1052 time to fit residues: 109.3672 Evaluate side-chains 721 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 633 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 498 HIS Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 110 TRP Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 498 HIS Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 312 THR Chi-restraints excluded: chain G residue 371 CYS Chi-restraints excluded: chain G residue 498 HIS Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 41 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN D 112 ASN F 112 ASN H 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.089969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.073099 restraints weight = 38573.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.075775 restraints weight = 19710.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.077711 restraints weight = 12615.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.079102 restraints weight = 9013.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.080059 restraints weight = 6997.595| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15228 Z= 0.204 Angle : 0.571 6.620 20644 Z= 0.309 Chirality : 0.039 0.209 2368 Planarity : 0.003 0.026 2576 Dihedral : 3.794 17.451 2104 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 7.73 % Allowed : 21.89 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.57 (0.20), residues: 1904 helix: 3.25 (0.13), residues: 1496 sheet: None (None), residues: 0 loop : -1.33 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 227 TYR 0.020 0.002 TYR E 268 PHE 0.018 0.002 PHE C 260 TRP 0.016 0.001 TRP E 369 HIS 0.005 0.001 HIS G 498 Details of bonding type rmsd covalent geometry : bond 0.00446 (15228) covalent geometry : angle 0.57136 (20644) hydrogen bonds : bond 0.03935 ( 1112) hydrogen bonds : angle 4.13215 ( 3336) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 636 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.8635 (t60) cc_final: 0.8173 (t60) REVERT: A 180 ARG cc_start: 0.8304 (mtt180) cc_final: 0.7810 (mmt-90) REVERT: A 227 ARG cc_start: 0.9287 (OUTLIER) cc_final: 0.7709 (ttp80) REVERT: A 240 LEU cc_start: 0.9229 (tt) cc_final: 0.8637 (tt) REVERT: A 291 ASP cc_start: 0.8443 (m-30) cc_final: 0.8160 (m-30) REVERT: A 308 LYS cc_start: 0.9107 (mttt) cc_final: 0.8731 (mttm) REVERT: A 355 ASN cc_start: 0.8520 (p0) cc_final: 0.8163 (p0) REVERT: A 369 TRP cc_start: 0.9055 (t60) cc_final: 0.8702 (t60) REVERT: A 499 HIS cc_start: 0.8355 (m-70) cc_final: 0.7932 (p-80) REVERT: A 526 ASP cc_start: 0.8977 (t70) cc_final: 0.8331 (t70) REVERT: A 533 GLN cc_start: 0.9234 (tm-30) cc_final: 0.8790 (tm-30) REVERT: A 534 TYR cc_start: 0.9289 (t80) cc_final: 0.8579 (t80) REVERT: A 536 GLN cc_start: 0.9580 (tt0) cc_final: 0.9262 (tt0) REVERT: B 9 GLN cc_start: 0.8830 (mp10) cc_final: 0.8386 (pt0) REVERT: B 12 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8370 (mm-30) REVERT: B 46 GLU cc_start: 0.9078 (tp30) cc_final: 0.8847 (tp30) REVERT: B 52 MET cc_start: 0.9243 (mtm) cc_final: 0.8807 (mtp) REVERT: B 54 ASN cc_start: 0.9287 (m-40) cc_final: 0.8953 (m110) REVERT: B 115 GLU cc_start: 0.8708 (mp0) cc_final: 0.8150 (mp0) REVERT: B 121 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8474 (mm-30) REVERT: B 124 GLU cc_start: 0.9181 (tp30) cc_final: 0.8883 (tp30) REVERT: B 125 MET cc_start: 0.9489 (ttt) cc_final: 0.9158 (ttt) REVERT: C 166 TRP cc_start: 0.8672 (t60) cc_final: 0.8237 (t60) REVERT: C 180 ARG cc_start: 0.8291 (mtt180) cc_final: 0.7778 (mmt-90) REVERT: C 227 ARG cc_start: 0.9283 (OUTLIER) cc_final: 0.7707 (ttp80) REVERT: C 291 ASP cc_start: 0.8441 (m-30) cc_final: 0.8153 (m-30) REVERT: C 308 LYS cc_start: 0.9100 (mttt) cc_final: 0.8723 (mttm) REVERT: C 355 ASN cc_start: 0.8520 (p0) cc_final: 0.8165 (p0) REVERT: C 369 TRP cc_start: 0.9050 (t60) cc_final: 0.8698 (t60) REVERT: C 499 HIS cc_start: 0.8357 (m-70) cc_final: 0.7932 (p-80) REVERT: C 526 ASP cc_start: 0.8979 (t70) cc_final: 0.8339 (t70) REVERT: C 533 GLN cc_start: 0.9256 (tm-30) cc_final: 0.8675 (tm-30) REVERT: C 534 TYR cc_start: 0.9269 (t80) cc_final: 0.8588 (t80) REVERT: C 536 GLN cc_start: 0.9578 (tt0) cc_final: 0.9266 (tt0) REVERT: D 9 GLN cc_start: 0.8830 (mp10) cc_final: 0.8384 (pt0) REVERT: D 12 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8375 (mm-30) REVERT: D 46 GLU cc_start: 0.9081 (tp30) cc_final: 0.8852 (tp30) REVERT: D 52 MET cc_start: 0.9239 (mtm) cc_final: 0.8808 (mtp) REVERT: D 54 ASN cc_start: 0.9285 (m-40) cc_final: 0.8951 (m110) REVERT: D 115 GLU cc_start: 0.8706 (mp0) cc_final: 0.8147 (mp0) REVERT: D 121 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8480 (mm-30) REVERT: D 124 GLU cc_start: 0.9180 (tp30) cc_final: 0.8881 (tp30) REVERT: D 125 MET cc_start: 0.9486 (ttt) cc_final: 0.9160 (ttt) REVERT: E 166 TRP cc_start: 0.8642 (t60) cc_final: 0.8181 (t60) REVERT: E 180 ARG cc_start: 0.8304 (mtt180) cc_final: 0.7813 (mmt-90) REVERT: E 227 ARG cc_start: 0.9282 (OUTLIER) cc_final: 0.7704 (ttp80) REVERT: E 240 LEU cc_start: 0.9233 (tt) cc_final: 0.8632 (tt) REVERT: E 291 ASP cc_start: 0.8448 (m-30) cc_final: 0.8164 (m-30) REVERT: E 308 LYS cc_start: 0.9109 (mttt) cc_final: 0.8733 (mttm) REVERT: E 355 ASN cc_start: 0.8521 (p0) cc_final: 0.8165 (p0) REVERT: E 369 TRP cc_start: 0.9048 (t60) cc_final: 0.8700 (t60) REVERT: E 499 HIS cc_start: 0.8355 (m-70) cc_final: 0.7932 (p-80) REVERT: E 526 ASP cc_start: 0.8977 (t70) cc_final: 0.8319 (t70) REVERT: E 533 GLN cc_start: 0.9255 (tm-30) cc_final: 0.8664 (tm-30) REVERT: E 534 TYR cc_start: 0.9271 (t80) cc_final: 0.8616 (t80) REVERT: E 536 GLN cc_start: 0.9579 (tt0) cc_final: 0.9271 (tt0) REVERT: F 9 GLN cc_start: 0.8829 (mp10) cc_final: 0.8385 (pt0) REVERT: F 12 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8357 (mm-30) REVERT: F 46 GLU cc_start: 0.9079 (tp30) cc_final: 0.8852 (tp30) REVERT: F 52 MET cc_start: 0.9241 (mtm) cc_final: 0.8809 (mtp) REVERT: F 54 ASN cc_start: 0.9281 (m-40) cc_final: 0.8946 (m110) REVERT: F 115 GLU cc_start: 0.8709 (mp0) cc_final: 0.8152 (mp0) REVERT: F 121 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8481 (mm-30) REVERT: F 124 GLU cc_start: 0.9181 (tp30) cc_final: 0.8880 (tp30) REVERT: F 125 MET cc_start: 0.9488 (ttt) cc_final: 0.9160 (ttt) REVERT: G 166 TRP cc_start: 0.8679 (t60) cc_final: 0.8243 (t60) REVERT: G 180 ARG cc_start: 0.8292 (mtt180) cc_final: 0.7780 (mmt-90) REVERT: G 227 ARG cc_start: 0.9286 (OUTLIER) cc_final: 0.7711 (ttp80) REVERT: G 291 ASP cc_start: 0.8445 (m-30) cc_final: 0.8157 (m-30) REVERT: G 308 LYS cc_start: 0.9102 (mttt) cc_final: 0.8725 (mttm) REVERT: G 355 ASN cc_start: 0.8527 (p0) cc_final: 0.8171 (p0) REVERT: G 369 TRP cc_start: 0.9058 (t60) cc_final: 0.8701 (t60) REVERT: G 499 HIS cc_start: 0.8350 (m-70) cc_final: 0.7931 (p-80) REVERT: G 526 ASP cc_start: 0.8978 (t70) cc_final: 0.8314 (t70) REVERT: G 533 GLN cc_start: 0.9255 (tm-30) cc_final: 0.8670 (tm-30) REVERT: G 534 TYR cc_start: 0.9266 (t80) cc_final: 0.8578 (t80) REVERT: G 536 GLN cc_start: 0.9579 (tt0) cc_final: 0.9266 (tt0) REVERT: H 9 GLN cc_start: 0.8826 (mp10) cc_final: 0.8384 (pt0) REVERT: H 12 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8351 (mm-30) REVERT: H 46 GLU cc_start: 0.9076 (tp30) cc_final: 0.8847 (tp30) REVERT: H 52 MET cc_start: 0.9239 (mtm) cc_final: 0.8807 (mtp) REVERT: H 54 ASN cc_start: 0.9289 (m-40) cc_final: 0.8953 (m110) REVERT: H 115 GLU cc_start: 0.8706 (mp0) cc_final: 0.8192 (mp0) REVERT: H 121 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8469 (mm-30) REVERT: H 124 GLU cc_start: 0.9181 (tp30) cc_final: 0.8879 (tp30) REVERT: H 125 MET cc_start: 0.9483 (ttt) cc_final: 0.9158 (ttt) outliers start: 112 outliers final: 92 residues processed: 675 average time/residue: 0.1055 time to fit residues: 109.2120 Evaluate side-chains 726 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 630 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 110 TRP Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 312 THR Chi-restraints excluded: chain G residue 371 CYS Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 178 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN D 112 ASN F 112 ASN H 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.089712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.073074 restraints weight = 39137.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.075813 restraints weight = 20051.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.077726 restraints weight = 12761.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.079111 restraints weight = 9148.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.080049 restraints weight = 7105.796| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15228 Z= 0.192 Angle : 0.569 7.448 20644 Z= 0.301 Chirality : 0.039 0.142 2368 Planarity : 0.004 0.035 2576 Dihedral : 3.700 17.662 2104 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 7.60 % Allowed : 23.14 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.55 (0.20), residues: 1904 helix: 3.15 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.13 (0.35), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 350 TYR 0.019 0.002 TYR A 268 PHE 0.018 0.002 PHE E 260 TRP 0.008 0.001 TRP G 295 HIS 0.004 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00421 (15228) covalent geometry : angle 0.56898 (20644) hydrogen bonds : bond 0.03867 ( 1112) hydrogen bonds : angle 4.08389 ( 3336) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 652 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ARG cc_start: 0.8163 (mtt180) cc_final: 0.7688 (mtt-85) REVERT: A 227 ARG cc_start: 0.9267 (OUTLIER) cc_final: 0.7667 (ttp80) REVERT: A 251 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8111 (mm-30) REVERT: A 291 ASP cc_start: 0.8469 (m-30) cc_final: 0.8207 (m-30) REVERT: A 308 LYS cc_start: 0.9072 (mttt) cc_final: 0.8731 (mttm) REVERT: A 355 ASN cc_start: 0.8579 (p0) cc_final: 0.8314 (p0) REVERT: A 369 TRP cc_start: 0.9129 (t60) cc_final: 0.8662 (t60) REVERT: A 499 HIS cc_start: 0.8337 (m-70) cc_final: 0.7956 (p-80) REVERT: A 526 ASP cc_start: 0.8994 (t70) cc_final: 0.8355 (t70) REVERT: A 533 GLN cc_start: 0.9295 (tm-30) cc_final: 0.8761 (tm-30) REVERT: A 534 TYR cc_start: 0.9259 (t80) cc_final: 0.8734 (t80) REVERT: A 536 GLN cc_start: 0.9585 (tt0) cc_final: 0.9276 (tt0) REVERT: B 12 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8451 (mm-30) REVERT: B 37 MET cc_start: 0.9489 (mmm) cc_final: 0.9249 (mmm) REVERT: B 46 GLU cc_start: 0.9119 (tp30) cc_final: 0.8896 (tp30) REVERT: B 52 MET cc_start: 0.9195 (mtm) cc_final: 0.8879 (mtp) REVERT: B 54 ASN cc_start: 0.9264 (m-40) cc_final: 0.8880 (m110) REVERT: B 72 MET cc_start: 0.9432 (ptm) cc_final: 0.9016 (tmm) REVERT: B 115 GLU cc_start: 0.8773 (mp0) cc_final: 0.8169 (mp0) REVERT: B 117 LEU cc_start: 0.9085 (mt) cc_final: 0.8637 (mt) REVERT: B 121 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8532 (mm-30) REVERT: B 124 GLU cc_start: 0.9205 (tp30) cc_final: 0.8869 (tp30) REVERT: B 125 MET cc_start: 0.9486 (ttt) cc_final: 0.9122 (ttt) REVERT: C 104 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9157 (tp) REVERT: C 180 ARG cc_start: 0.8347 (mtt180) cc_final: 0.7806 (mtt-85) REVERT: C 227 ARG cc_start: 0.9274 (OUTLIER) cc_final: 0.7716 (ttp80) REVERT: C 251 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8309 (mm-30) REVERT: C 291 ASP cc_start: 0.8466 (m-30) cc_final: 0.8203 (m-30) REVERT: C 308 LYS cc_start: 0.9065 (mttt) cc_final: 0.8717 (mttm) REVERT: C 355 ASN cc_start: 0.8585 (p0) cc_final: 0.8327 (p0) REVERT: C 369 TRP cc_start: 0.9129 (t60) cc_final: 0.8650 (t60) REVERT: C 499 HIS cc_start: 0.8339 (m-70) cc_final: 0.7958 (p-80) REVERT: C 526 ASP cc_start: 0.9004 (t70) cc_final: 0.8374 (t70) REVERT: C 533 GLN cc_start: 0.9239 (tm-30) cc_final: 0.9028 (tm-30) REVERT: C 534 TYR cc_start: 0.9253 (t80) cc_final: 0.8708 (t80) REVERT: C 536 GLN cc_start: 0.9578 (tt0) cc_final: 0.9268 (tt0) REVERT: D 12 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8447 (mm-30) REVERT: D 37 MET cc_start: 0.9493 (mmm) cc_final: 0.9250 (mmm) REVERT: D 46 GLU cc_start: 0.9121 (tp30) cc_final: 0.8899 (tp30) REVERT: D 52 MET cc_start: 0.9198 (mtm) cc_final: 0.8881 (mtp) REVERT: D 54 ASN cc_start: 0.9263 (m-40) cc_final: 0.8879 (m110) REVERT: D 72 MET cc_start: 0.9428 (ptm) cc_final: 0.9017 (tmm) REVERT: D 115 GLU cc_start: 0.8771 (mp0) cc_final: 0.8166 (mp0) REVERT: D 117 LEU cc_start: 0.9083 (mt) cc_final: 0.8636 (mt) REVERT: D 121 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8522 (mm-30) REVERT: D 124 GLU cc_start: 0.9199 (tp30) cc_final: 0.8860 (tp30) REVERT: D 125 MET cc_start: 0.9463 (ttt) cc_final: 0.9139 (ttt) REVERT: E 180 ARG cc_start: 0.8165 (mtt180) cc_final: 0.7691 (mtt-85) REVERT: E 227 ARG cc_start: 0.9273 (OUTLIER) cc_final: 0.7716 (ttp80) REVERT: E 251 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8106 (mm-30) REVERT: E 291 ASP cc_start: 0.8467 (m-30) cc_final: 0.8208 (m-30) REVERT: E 308 LYS cc_start: 0.9075 (mttt) cc_final: 0.8732 (mttm) REVERT: E 355 ASN cc_start: 0.8585 (p0) cc_final: 0.8324 (p0) REVERT: E 369 TRP cc_start: 0.9129 (t60) cc_final: 0.8674 (t60) REVERT: E 499 HIS cc_start: 0.8335 (m-70) cc_final: 0.7955 (p-80) REVERT: E 526 ASP cc_start: 0.8994 (t70) cc_final: 0.8357 (t70) REVERT: E 533 GLN cc_start: 0.9237 (tm-30) cc_final: 0.9028 (tm-30) REVERT: E 534 TYR cc_start: 0.9251 (t80) cc_final: 0.8721 (t80) REVERT: E 536 GLN cc_start: 0.9574 (tt0) cc_final: 0.9264 (tt0) REVERT: F 12 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8438 (mm-30) REVERT: F 37 MET cc_start: 0.9493 (mmm) cc_final: 0.9248 (mmm) REVERT: F 46 GLU cc_start: 0.9122 (tp30) cc_final: 0.8903 (tp30) REVERT: F 52 MET cc_start: 0.9194 (mtm) cc_final: 0.8880 (mtp) REVERT: F 54 ASN cc_start: 0.9264 (m-40) cc_final: 0.8879 (m110) REVERT: F 72 MET cc_start: 0.9430 (ptm) cc_final: 0.9018 (tmm) REVERT: F 115 GLU cc_start: 0.8776 (mp0) cc_final: 0.8171 (mp0) REVERT: F 117 LEU cc_start: 0.9083 (mt) cc_final: 0.8634 (mt) REVERT: F 121 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8529 (mm-30) REVERT: F 124 GLU cc_start: 0.9203 (tp30) cc_final: 0.8869 (tp30) REVERT: F 125 MET cc_start: 0.9483 (ttt) cc_final: 0.9122 (ttt) REVERT: G 104 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9023 (tp) REVERT: G 180 ARG cc_start: 0.8129 (mtt180) cc_final: 0.7648 (mtt-85) REVERT: G 227 ARG cc_start: 0.9275 (OUTLIER) cc_final: 0.7712 (ttp80) REVERT: G 251 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8300 (mm-30) REVERT: G 291 ASP cc_start: 0.8470 (m-30) cc_final: 0.8208 (m-30) REVERT: G 308 LYS cc_start: 0.9069 (mttt) cc_final: 0.8722 (mttm) REVERT: G 355 ASN cc_start: 0.8585 (p0) cc_final: 0.8324 (p0) REVERT: G 369 TRP cc_start: 0.9132 (t60) cc_final: 0.8668 (t60) REVERT: G 499 HIS cc_start: 0.8334 (m-70) cc_final: 0.7956 (p-80) REVERT: G 526 ASP cc_start: 0.8988 (t70) cc_final: 0.8349 (t70) REVERT: G 533 GLN cc_start: 0.9236 (tm-30) cc_final: 0.9033 (tm-30) REVERT: G 534 TYR cc_start: 0.9273 (t80) cc_final: 0.8669 (t80) REVERT: G 536 GLN cc_start: 0.9578 (tt0) cc_final: 0.9267 (tt0) REVERT: H 12 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8434 (mm-30) REVERT: H 37 MET cc_start: 0.9495 (mmm) cc_final: 0.9253 (mmm) REVERT: H 46 GLU cc_start: 0.9120 (tp30) cc_final: 0.8900 (tp30) REVERT: H 52 MET cc_start: 0.9193 (mtm) cc_final: 0.8877 (mtp) REVERT: H 54 ASN cc_start: 0.9266 (m-40) cc_final: 0.8881 (m110) REVERT: H 72 MET cc_start: 0.9425 (ptm) cc_final: 0.9014 (tmm) REVERT: H 115 GLU cc_start: 0.8767 (mp0) cc_final: 0.8160 (mp0) REVERT: H 117 LEU cc_start: 0.9083 (mt) cc_final: 0.8634 (mt) REVERT: H 121 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8531 (mm-30) REVERT: H 124 GLU cc_start: 0.9205 (tp30) cc_final: 0.8867 (tp30) REVERT: H 125 MET cc_start: 0.9486 (ttt) cc_final: 0.9120 (ttt) outliers start: 110 outliers final: 78 residues processed: 691 average time/residue: 0.1148 time to fit residues: 118.7228 Evaluate side-chains 718 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 630 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 532 GLU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 110 TRP Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 532 GLU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 251 GLU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 312 THR Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 532 GLU Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 88 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 157 optimal weight: 0.1980 chunk 36 optimal weight: 4.9990 chunk 82 optimal weight: 0.2980 chunk 17 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 186 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN D 112 ASN F 112 ASN H 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.092170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.075626 restraints weight = 38223.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.078400 restraints weight = 19436.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.080321 restraints weight = 12290.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.081725 restraints weight = 8795.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.082723 restraints weight = 6808.689| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15228 Z= 0.125 Angle : 0.595 9.903 20644 Z= 0.297 Chirality : 0.040 0.273 2368 Planarity : 0.003 0.041 2576 Dihedral : 3.634 17.690 2104 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 5.18 % Allowed : 26.24 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.63 (0.20), residues: 1904 helix: 3.25 (0.13), residues: 1492 sheet: None (None), residues: 0 loop : -1.07 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 127 TYR 0.016 0.002 TYR E 268 PHE 0.018 0.001 PHE A 260 TRP 0.008 0.001 TRP G 295 HIS 0.005 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00280 (15228) covalent geometry : angle 0.59491 (20644) hydrogen bonds : bond 0.03607 ( 1112) hydrogen bonds : angle 3.88046 ( 3336) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 653 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.8552 (t60) cc_final: 0.8115 (t60) REVERT: A 180 ARG cc_start: 0.8198 (mtt180) cc_final: 0.7605 (mtt-85) REVERT: A 227 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.7655 (ttp80) REVERT: A 240 LEU cc_start: 0.9018 (tt) cc_final: 0.8084 (tt) REVERT: A 251 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8242 (mm-30) REVERT: A 291 ASP cc_start: 0.8418 (m-30) cc_final: 0.8179 (m-30) REVERT: A 308 LYS cc_start: 0.9012 (mttt) cc_final: 0.8663 (mttm) REVERT: A 355 ASN cc_start: 0.8526 (p0) cc_final: 0.8270 (p0) REVERT: A 369 TRP cc_start: 0.9104 (t60) cc_final: 0.8575 (t60) REVERT: A 499 HIS cc_start: 0.8422 (m-70) cc_final: 0.7914 (p-80) REVERT: A 526 ASP cc_start: 0.8929 (t70) cc_final: 0.8221 (t70) REVERT: A 534 TYR cc_start: 0.9137 (t80) cc_final: 0.8642 (t80) REVERT: B 9 GLN cc_start: 0.8888 (mp10) cc_final: 0.8627 (pm20) REVERT: B 12 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8488 (mm-30) REVERT: B 37 MET cc_start: 0.9485 (mmm) cc_final: 0.9171 (mmm) REVERT: B 46 GLU cc_start: 0.9114 (tp30) cc_final: 0.8869 (tp30) REVERT: B 52 MET cc_start: 0.9203 (mtm) cc_final: 0.8812 (mtm) REVERT: B 54 ASN cc_start: 0.9283 (m-40) cc_final: 0.8838 (m110) REVERT: B 72 MET cc_start: 0.9452 (OUTLIER) cc_final: 0.8943 (tmm) REVERT: B 91 ARG cc_start: 0.8601 (ttm170) cc_final: 0.8321 (ttm110) REVERT: B 115 GLU cc_start: 0.8751 (mp0) cc_final: 0.8337 (mp0) REVERT: B 117 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8456 (mt) REVERT: B 121 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8493 (mm-30) REVERT: B 124 GLU cc_start: 0.9198 (tp30) cc_final: 0.8856 (tp30) REVERT: B 125 MET cc_start: 0.9487 (ttt) cc_final: 0.9169 (ttt) REVERT: C 104 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9046 (tp) REVERT: C 166 TRP cc_start: 0.8614 (t60) cc_final: 0.8153 (t60) REVERT: C 180 ARG cc_start: 0.8130 (mtt180) cc_final: 0.7476 (mtt-85) REVERT: C 227 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.7667 (ttp80) REVERT: C 229 LEU cc_start: 0.9742 (mt) cc_final: 0.9534 (mm) REVERT: C 240 LEU cc_start: 0.9022 (tt) cc_final: 0.8072 (tt) REVERT: C 251 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8244 (mm-30) REVERT: C 291 ASP cc_start: 0.8415 (m-30) cc_final: 0.8177 (m-30) REVERT: C 308 LYS cc_start: 0.8950 (mttt) cc_final: 0.8619 (mttm) REVERT: C 343 LEU cc_start: 0.8986 (mt) cc_final: 0.8567 (mp) REVERT: C 355 ASN cc_start: 0.8528 (p0) cc_final: 0.8275 (p0) REVERT: C 369 TRP cc_start: 0.9096 (t60) cc_final: 0.8574 (t60) REVERT: C 499 HIS cc_start: 0.8425 (m-70) cc_final: 0.7915 (p-80) REVERT: C 526 ASP cc_start: 0.8948 (t70) cc_final: 0.8229 (t70) REVERT: C 534 TYR cc_start: 0.9145 (t80) cc_final: 0.8632 (t80) REVERT: D 9 GLN cc_start: 0.8888 (mp10) cc_final: 0.8627 (pm20) REVERT: D 12 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8497 (mm-30) REVERT: D 37 MET cc_start: 0.9485 (mmm) cc_final: 0.9179 (mmm) REVERT: D 46 GLU cc_start: 0.9116 (tp30) cc_final: 0.8871 (tp30) REVERT: D 52 MET cc_start: 0.9211 (mtm) cc_final: 0.8820 (mtm) REVERT: D 54 ASN cc_start: 0.9279 (m-40) cc_final: 0.8835 (m110) REVERT: D 72 MET cc_start: 0.9447 (OUTLIER) cc_final: 0.8944 (tmm) REVERT: D 91 ARG cc_start: 0.8603 (ttm170) cc_final: 0.8323 (ttm110) REVERT: D 115 GLU cc_start: 0.8752 (mp0) cc_final: 0.8338 (mp0) REVERT: D 117 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8452 (mt) REVERT: D 121 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8489 (mm-30) REVERT: D 124 GLU cc_start: 0.9200 (tp30) cc_final: 0.8860 (tp30) REVERT: D 125 MET cc_start: 0.9493 (ttt) cc_final: 0.9166 (ttt) REVERT: E 166 TRP cc_start: 0.8565 (t60) cc_final: 0.8131 (t60) REVERT: E 180 ARG cc_start: 0.8202 (mtt180) cc_final: 0.7610 (mtt-85) REVERT: E 227 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.7655 (ttp80) REVERT: E 240 LEU cc_start: 0.9025 (tt) cc_final: 0.8078 (tt) REVERT: E 251 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8244 (mm-30) REVERT: E 291 ASP cc_start: 0.8420 (m-30) cc_final: 0.8183 (m-30) REVERT: E 308 LYS cc_start: 0.9015 (mttt) cc_final: 0.8665 (mttm) REVERT: E 355 ASN cc_start: 0.8530 (p0) cc_final: 0.8276 (p0) REVERT: E 369 TRP cc_start: 0.9095 (t60) cc_final: 0.8575 (t60) REVERT: E 499 HIS cc_start: 0.8422 (m-70) cc_final: 0.7911 (p-80) REVERT: E 526 ASP cc_start: 0.8930 (t70) cc_final: 0.8210 (t70) REVERT: E 534 TYR cc_start: 0.9146 (t80) cc_final: 0.8654 (t80) REVERT: F 9 GLN cc_start: 0.8885 (mp10) cc_final: 0.8624 (pm20) REVERT: F 12 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8487 (mm-30) REVERT: F 37 MET cc_start: 0.9486 (mmm) cc_final: 0.9179 (mmm) REVERT: F 46 GLU cc_start: 0.9115 (tp30) cc_final: 0.8870 (tp30) REVERT: F 52 MET cc_start: 0.9208 (mtm) cc_final: 0.8820 (mtm) REVERT: F 54 ASN cc_start: 0.9282 (m-40) cc_final: 0.8858 (m110) REVERT: F 72 MET cc_start: 0.9446 (OUTLIER) cc_final: 0.8943 (tmm) REVERT: F 91 ARG cc_start: 0.8600 (ttm170) cc_final: 0.8322 (ttm110) REVERT: F 115 GLU cc_start: 0.8753 (mp0) cc_final: 0.8340 (mp0) REVERT: F 117 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8453 (mt) REVERT: F 121 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8495 (mm-30) REVERT: F 124 GLU cc_start: 0.9198 (tp30) cc_final: 0.8858 (tp30) REVERT: F 125 MET cc_start: 0.9491 (ttt) cc_final: 0.9173 (ttt) REVERT: G 104 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9043 (tp) REVERT: G 166 TRP cc_start: 0.8612 (t60) cc_final: 0.8150 (t60) REVERT: G 180 ARG cc_start: 0.8129 (mtt180) cc_final: 0.7474 (mtt-85) REVERT: G 227 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.7669 (ttp80) REVERT: G 229 LEU cc_start: 0.9742 (mt) cc_final: 0.9536 (mm) REVERT: G 240 LEU cc_start: 0.9017 (tt) cc_final: 0.8073 (tt) REVERT: G 251 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8251 (mm-30) REVERT: G 291 ASP cc_start: 0.8424 (m-30) cc_final: 0.8182 (m-30) REVERT: G 308 LYS cc_start: 0.8955 (mttt) cc_final: 0.8623 (mttm) REVERT: G 343 LEU cc_start: 0.8999 (mt) cc_final: 0.8590 (mp) REVERT: G 355 ASN cc_start: 0.8526 (p0) cc_final: 0.8271 (p0) REVERT: G 369 TRP cc_start: 0.9111 (t60) cc_final: 0.8585 (t60) REVERT: G 499 HIS cc_start: 0.8421 (m-70) cc_final: 0.7914 (p-80) REVERT: G 526 ASP cc_start: 0.8926 (t70) cc_final: 0.8207 (t70) REVERT: G 534 TYR cc_start: 0.9161 (t80) cc_final: 0.8666 (t80) REVERT: H 9 GLN cc_start: 0.8884 (mp10) cc_final: 0.8623 (pm20) REVERT: H 12 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8483 (mm-30) REVERT: H 37 MET cc_start: 0.9486 (mmm) cc_final: 0.9173 (mmm) REVERT: H 46 GLU cc_start: 0.9116 (tp30) cc_final: 0.8872 (tp30) REVERT: H 52 MET cc_start: 0.9200 (mtm) cc_final: 0.8814 (mtm) REVERT: H 54 ASN cc_start: 0.9284 (m-40) cc_final: 0.8839 (m110) REVERT: H 72 MET cc_start: 0.9446 (OUTLIER) cc_final: 0.8939 (tmm) REVERT: H 91 ARG cc_start: 0.8601 (ttm170) cc_final: 0.8322 (ttm110) REVERT: H 115 GLU cc_start: 0.8746 (mp0) cc_final: 0.8330 (mp0) REVERT: H 117 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8452 (mt) REVERT: H 121 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8494 (mm-30) REVERT: H 124 GLU cc_start: 0.9200 (tp30) cc_final: 0.8858 (tp30) REVERT: H 125 MET cc_start: 0.9489 (ttt) cc_final: 0.9170 (ttt) outliers start: 75 outliers final: 35 residues processed: 678 average time/residue: 0.1107 time to fit residues: 114.0975 Evaluate side-chains 698 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 645 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 498 HIS Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain E residue 110 TRP Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain E residue 498 HIS Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 251 GLU Chi-restraints excluded: chain G residue 498 HIS Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 146 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 14 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 38 optimal weight: 0.3980 chunk 181 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 85 optimal weight: 0.1980 chunk 92 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 97 optimal weight: 0.4980 chunk 41 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN D 112 ASN F 112 ASN H 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.091783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.075162 restraints weight = 38356.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.077980 restraints weight = 19194.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.079929 restraints weight = 11998.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.081342 restraints weight = 8528.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.082282 restraints weight = 6575.722| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15228 Z= 0.136 Angle : 0.583 9.131 20644 Z= 0.294 Chirality : 0.039 0.199 2368 Planarity : 0.003 0.038 2576 Dihedral : 3.520 18.432 2104 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.11 % Allowed : 26.24 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.56 (0.20), residues: 1904 helix: 3.19 (0.13), residues: 1492 sheet: None (None), residues: 0 loop : -1.06 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 75 TYR 0.018 0.002 TYR E 268 PHE 0.017 0.001 PHE C 260 TRP 0.008 0.001 TRP G 295 HIS 0.004 0.001 HIS F 108 Details of bonding type rmsd covalent geometry : bond 0.00308 (15228) covalent geometry : angle 0.58287 (20644) hydrogen bonds : bond 0.03453 ( 1112) hydrogen bonds : angle 3.87819 ( 3336) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 669 time to evaluate : 0.590 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 166 TRP cc_start: 0.8526 (t60) cc_final: 0.8029 (t60) REVERT: A 180 ARG cc_start: 0.8229 (mtt180) cc_final: 0.7662 (mmt-90) REVERT: A 193 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9220 (mp) REVERT: A 227 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.7612 (ttp80) REVERT: A 240 LEU cc_start: 0.9008 (tt) cc_final: 0.8537 (tt) REVERT: A 251 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8429 (mm-30) REVERT: A 291 ASP cc_start: 0.8408 (m-30) cc_final: 0.8179 (m-30) REVERT: A 308 LYS cc_start: 0.8986 (mttt) cc_final: 0.8632 (mttm) REVERT: A 355 ASN cc_start: 0.8522 (p0) cc_final: 0.8215 (p0) REVERT: A 369 TRP cc_start: 0.9065 (t60) cc_final: 0.8601 (t60) REVERT: A 499 HIS cc_start: 0.8451 (m-70) cc_final: 0.7969 (p-80) REVERT: A 526 ASP cc_start: 0.8977 (t70) cc_final: 0.8284 (t70) REVERT: A 534 TYR cc_start: 0.9220 (t80) cc_final: 0.8985 (t80) REVERT: B 9 GLN cc_start: 0.8839 (mp10) cc_final: 0.8558 (pm20) REVERT: B 12 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8523 (mm-30) REVERT: B 37 MET cc_start: 0.9457 (mmm) cc_final: 0.9157 (mmm) REVERT: B 52 MET cc_start: 0.9237 (mtm) cc_final: 0.8831 (mtm) REVERT: B 54 ASN cc_start: 0.9269 (m-40) cc_final: 0.8810 (m110) REVERT: B 72 MET cc_start: 0.9525 (OUTLIER) cc_final: 0.9016 (tmm) REVERT: B 91 ARG cc_start: 0.8576 (ttm170) cc_final: 0.8281 (ttm110) REVERT: B 115 GLU cc_start: 0.8753 (mp0) cc_final: 0.8336 (mp0) REVERT: B 117 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8438 (mt) REVERT: B 121 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8550 (mm-30) REVERT: B 125 MET cc_start: 0.9515 (ttt) cc_final: 0.9186 (ttt) REVERT: B 127 ARG cc_start: 0.9244 (ttm110) cc_final: 0.9026 (ttp-110) REVERT: C 104 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8889 (tp) REVERT: C 166 TRP cc_start: 0.8545 (t60) cc_final: 0.8013 (t60) REVERT: C 180 ARG cc_start: 0.8227 (mtt180) cc_final: 0.7657 (mmt-90) REVERT: C 227 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.7645 (ttp80) REVERT: C 229 LEU cc_start: 0.9756 (mt) cc_final: 0.9533 (mm) REVERT: C 240 LEU cc_start: 0.9017 (tt) cc_final: 0.8537 (tt) REVERT: C 251 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8506 (mm-30) REVERT: C 291 ASP cc_start: 0.8411 (m-30) cc_final: 0.8185 (m-30) REVERT: C 308 LYS cc_start: 0.8927 (mttt) cc_final: 0.8584 (mttm) REVERT: C 355 ASN cc_start: 0.8529 (p0) cc_final: 0.8250 (p0) REVERT: C 369 TRP cc_start: 0.9062 (t60) cc_final: 0.8600 (t60) REVERT: C 499 HIS cc_start: 0.8452 (m-70) cc_final: 0.7971 (p-80) REVERT: C 526 ASP cc_start: 0.8999 (t70) cc_final: 0.8317 (t70) REVERT: D 9 GLN cc_start: 0.8838 (mp10) cc_final: 0.8558 (pm20) REVERT: D 12 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8526 (mm-30) REVERT: D 37 MET cc_start: 0.9453 (mmm) cc_final: 0.9154 (mmm) REVERT: D 52 MET cc_start: 0.9241 (mtm) cc_final: 0.8830 (mtm) REVERT: D 54 ASN cc_start: 0.9265 (m-40) cc_final: 0.8805 (m110) REVERT: D 72 MET cc_start: 0.9525 (OUTLIER) cc_final: 0.9017 (tmm) REVERT: D 91 ARG cc_start: 0.8580 (ttm170) cc_final: 0.8286 (ttm110) REVERT: D 115 GLU cc_start: 0.8755 (mp0) cc_final: 0.8337 (mp0) REVERT: D 117 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8434 (mt) REVERT: D 121 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8551 (mm-30) REVERT: D 125 MET cc_start: 0.9511 (ttt) cc_final: 0.9188 (ttt) REVERT: D 127 ARG cc_start: 0.9244 (ttm110) cc_final: 0.9026 (ttp-110) REVERT: E 166 TRP cc_start: 0.8543 (t60) cc_final: 0.8049 (t60) REVERT: E 180 ARG cc_start: 0.8235 (mtt180) cc_final: 0.7669 (mmt-90) REVERT: E 193 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9222 (mp) REVERT: E 227 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.7610 (ttp80) REVERT: E 240 LEU cc_start: 0.9024 (tt) cc_final: 0.8539 (tt) REVERT: E 251 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8437 (mm-30) REVERT: E 291 ASP cc_start: 0.8414 (m-30) cc_final: 0.8187 (m-30) REVERT: E 308 LYS cc_start: 0.8992 (mttt) cc_final: 0.8634 (mttm) REVERT: E 355 ASN cc_start: 0.8529 (p0) cc_final: 0.8228 (p0) REVERT: E 369 TRP cc_start: 0.9056 (t60) cc_final: 0.8606 (t60) REVERT: E 499 HIS cc_start: 0.8448 (m-70) cc_final: 0.7965 (p-80) REVERT: E 526 ASP cc_start: 0.8988 (t70) cc_final: 0.8298 (t70) REVERT: F 9 GLN cc_start: 0.8837 (mp10) cc_final: 0.8557 (pm20) REVERT: F 12 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8528 (mm-30) REVERT: F 37 MET cc_start: 0.9456 (mmm) cc_final: 0.9156 (mmm) REVERT: F 52 MET cc_start: 0.9222 (mtm) cc_final: 0.8795 (mtm) REVERT: F 54 ASN cc_start: 0.9268 (m-40) cc_final: 0.8806 (m110) REVERT: F 72 MET cc_start: 0.9525 (OUTLIER) cc_final: 0.9018 (tmm) REVERT: F 91 ARG cc_start: 0.8579 (ttm170) cc_final: 0.8286 (ttm110) REVERT: F 115 GLU cc_start: 0.8756 (mp0) cc_final: 0.8341 (mp0) REVERT: F 117 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8434 (mt) REVERT: F 121 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8555 (mm-30) REVERT: F 125 MET cc_start: 0.9520 (ttt) cc_final: 0.9190 (ttt) REVERT: F 127 ARG cc_start: 0.9235 (ttm110) cc_final: 0.9016 (ttp-110) REVERT: G 104 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8873 (tp) REVERT: G 166 TRP cc_start: 0.8541 (t60) cc_final: 0.8008 (t60) REVERT: G 180 ARG cc_start: 0.8226 (mtt180) cc_final: 0.7653 (mmt-90) REVERT: G 227 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.7646 (ttp80) REVERT: G 229 LEU cc_start: 0.9756 (mt) cc_final: 0.9534 (mm) REVERT: G 240 LEU cc_start: 0.9013 (tt) cc_final: 0.8533 (tt) REVERT: G 251 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8448 (mm-30) REVERT: G 291 ASP cc_start: 0.8415 (m-30) cc_final: 0.8187 (m-30) REVERT: G 308 LYS cc_start: 0.8933 (mttt) cc_final: 0.8591 (mttm) REVERT: G 355 ASN cc_start: 0.8529 (p0) cc_final: 0.8267 (p0) REVERT: G 369 TRP cc_start: 0.9067 (t60) cc_final: 0.8611 (t60) REVERT: G 499 HIS cc_start: 0.8452 (m-70) cc_final: 0.7971 (p-80) REVERT: G 526 ASP cc_start: 0.8982 (t70) cc_final: 0.8289 (t70) REVERT: H 9 GLN cc_start: 0.8838 (mp10) cc_final: 0.8557 (pm20) REVERT: H 12 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8522 (mm-30) REVERT: H 37 MET cc_start: 0.9457 (mmm) cc_final: 0.9156 (mmm) REVERT: H 52 MET cc_start: 0.9236 (mtm) cc_final: 0.8828 (mtm) REVERT: H 54 ASN cc_start: 0.9269 (m-40) cc_final: 0.8808 (m110) REVERT: H 72 MET cc_start: 0.9524 (OUTLIER) cc_final: 0.9015 (tmm) REVERT: H 91 ARG cc_start: 0.8575 (ttm170) cc_final: 0.8280 (ttm110) REVERT: H 115 GLU cc_start: 0.8750 (mp0) cc_final: 0.8330 (mp0) REVERT: H 117 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8438 (mt) REVERT: H 121 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8547 (mm-30) REVERT: H 125 MET cc_start: 0.9520 (ttt) cc_final: 0.9189 (ttt) REVERT: H 127 ARG cc_start: 0.9236 (ttm110) cc_final: 0.9017 (ttp-110) outliers start: 74 outliers final: 42 residues processed: 691 average time/residue: 0.1099 time to fit residues: 115.5515 Evaluate side-chains 693 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 631 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 498 HIS Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain E residue 110 TRP Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 498 HIS Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 251 GLU Chi-restraints excluded: chain G residue 498 HIS Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 146 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 12 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 133 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 113 optimal weight: 7.9990 chunk 119 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN F 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.091765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.075545 restraints weight = 38373.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.078337 restraints weight = 19329.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.080277 restraints weight = 12084.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.081655 restraints weight = 8541.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.082631 restraints weight = 6571.715| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15228 Z= 0.137 Angle : 0.598 9.834 20644 Z= 0.300 Chirality : 0.039 0.214 2368 Planarity : 0.003 0.036 2576 Dihedral : 3.531 17.894 2104 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.90 % Allowed : 27.49 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.46 (0.20), residues: 1904 helix: 3.12 (0.13), residues: 1492 sheet: None (None), residues: 0 loop : -1.09 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 350 TYR 0.029 0.002 TYR C 534 PHE 0.031 0.002 PHE F 66 TRP 0.008 0.001 TRP G 295 HIS 0.004 0.001 HIS F 108 Details of bonding type rmsd covalent geometry : bond 0.00315 (15228) covalent geometry : angle 0.59786 (20644) hydrogen bonds : bond 0.03511 ( 1112) hydrogen bonds : angle 3.86790 ( 3336) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 642 time to evaluate : 0.572 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 166 TRP cc_start: 0.8562 (t60) cc_final: 0.8102 (t60) REVERT: A 180 ARG cc_start: 0.8284 (mtt180) cc_final: 0.7710 (mmt-90) REVERT: A 227 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.7537 (ttp80) REVERT: A 291 ASP cc_start: 0.8424 (m-30) cc_final: 0.8205 (m-30) REVERT: A 308 LYS cc_start: 0.8941 (mttt) cc_final: 0.8607 (mttm) REVERT: A 369 TRP cc_start: 0.9145 (t60) cc_final: 0.8764 (t60) REVERT: A 499 HIS cc_start: 0.8466 (m-70) cc_final: 0.7984 (p-80) REVERT: A 526 ASP cc_start: 0.8950 (t70) cc_final: 0.8243 (t70) REVERT: A 533 GLN cc_start: 0.9290 (tm-30) cc_final: 0.9082 (tm-30) REVERT: A 534 TYR cc_start: 0.9041 (t80) cc_final: 0.8734 (t80) REVERT: B 9 GLN cc_start: 0.8887 (mp10) cc_final: 0.8630 (pm20) REVERT: B 12 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8425 (mm-30) REVERT: B 14 LYS cc_start: 0.8811 (tptp) cc_final: 0.8540 (tppt) REVERT: B 37 MET cc_start: 0.9443 (mmm) cc_final: 0.9148 (mmm) REVERT: B 52 MET cc_start: 0.9202 (mtm) cc_final: 0.8782 (mtm) REVERT: B 54 ASN cc_start: 0.9272 (m-40) cc_final: 0.8810 (m110) REVERT: B 72 MET cc_start: 0.9494 (OUTLIER) cc_final: 0.8997 (tmm) REVERT: B 91 ARG cc_start: 0.8669 (ttm170) cc_final: 0.8466 (ttm-80) REVERT: B 115 GLU cc_start: 0.8718 (mp0) cc_final: 0.8322 (mp0) REVERT: B 117 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8372 (mt) REVERT: B 121 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8428 (mm-30) REVERT: B 125 MET cc_start: 0.9497 (ttt) cc_final: 0.9163 (ttt) REVERT: C 104 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8983 (tp) REVERT: C 166 TRP cc_start: 0.8609 (t60) cc_final: 0.8098 (t60) REVERT: C 180 ARG cc_start: 0.8276 (mtt180) cc_final: 0.7697 (mmt-90) REVERT: C 227 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8883 (ttm-80) REVERT: C 229 LEU cc_start: 0.9776 (mt) cc_final: 0.9576 (mm) REVERT: C 291 ASP cc_start: 0.8423 (m-30) cc_final: 0.8202 (m-30) REVERT: C 308 LYS cc_start: 0.8943 (mttt) cc_final: 0.8621 (mttm) REVERT: C 355 ASN cc_start: 0.8513 (p0) cc_final: 0.8274 (p0) REVERT: C 369 TRP cc_start: 0.9143 (t60) cc_final: 0.8767 (t60) REVERT: C 499 HIS cc_start: 0.8469 (m-70) cc_final: 0.7987 (p-80) REVERT: C 526 ASP cc_start: 0.9002 (t70) cc_final: 0.8344 (t70) REVERT: D 9 GLN cc_start: 0.8888 (mp10) cc_final: 0.8632 (pm20) REVERT: D 12 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8422 (mm-30) REVERT: D 14 LYS cc_start: 0.8813 (tptp) cc_final: 0.8542 (tppt) REVERT: D 37 MET cc_start: 0.9445 (mmm) cc_final: 0.9149 (mmm) REVERT: D 52 MET cc_start: 0.9202 (mtm) cc_final: 0.8780 (mtm) REVERT: D 54 ASN cc_start: 0.9268 (m-40) cc_final: 0.8804 (m110) REVERT: D 72 MET cc_start: 0.9493 (OUTLIER) cc_final: 0.8993 (tmm) REVERT: D 91 ARG cc_start: 0.8662 (ttm170) cc_final: 0.8406 (ttm110) REVERT: D 115 GLU cc_start: 0.8754 (mp0) cc_final: 0.8344 (mp0) REVERT: D 117 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8373 (mt) REVERT: D 121 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8430 (mm-30) REVERT: D 124 GLU cc_start: 0.9166 (tp30) cc_final: 0.8965 (tp30) REVERT: D 125 MET cc_start: 0.9498 (ttt) cc_final: 0.9163 (ttt) REVERT: E 166 TRP cc_start: 0.8567 (t60) cc_final: 0.8110 (t60) REVERT: E 180 ARG cc_start: 0.8286 (mtt180) cc_final: 0.7713 (mmt-90) REVERT: E 227 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.7534 (ttp80) REVERT: E 291 ASP cc_start: 0.8424 (m-30) cc_final: 0.8204 (m-30) REVERT: E 308 LYS cc_start: 0.8949 (mttt) cc_final: 0.8610 (mttm) REVERT: E 369 TRP cc_start: 0.9140 (t60) cc_final: 0.8771 (t60) REVERT: E 499 HIS cc_start: 0.8463 (m-70) cc_final: 0.7980 (p-80) REVERT: E 526 ASP cc_start: 0.8994 (t70) cc_final: 0.8330 (t70) REVERT: E 534 TYR cc_start: 0.9048 (t80) cc_final: 0.8382 (t80) REVERT: F 9 GLN cc_start: 0.8887 (mp10) cc_final: 0.8629 (pm20) REVERT: F 12 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8431 (mm-30) REVERT: F 14 LYS cc_start: 0.8807 (tptp) cc_final: 0.8537 (tppt) REVERT: F 37 MET cc_start: 0.9446 (mmm) cc_final: 0.9153 (mmm) REVERT: F 52 MET cc_start: 0.9210 (mtm) cc_final: 0.8784 (mtm) REVERT: F 54 ASN cc_start: 0.9268 (m-40) cc_final: 0.8791 (m110) REVERT: F 72 MET cc_start: 0.9498 (OUTLIER) cc_final: 0.8994 (tmm) REVERT: F 115 GLU cc_start: 0.8720 (mp0) cc_final: 0.8323 (mp0) REVERT: F 117 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8368 (mt) REVERT: F 121 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8426 (mm-30) REVERT: F 125 MET cc_start: 0.9500 (ttt) cc_final: 0.9168 (ttt) REVERT: G 104 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8976 (tp) REVERT: G 166 TRP cc_start: 0.8614 (t60) cc_final: 0.8104 (t60) REVERT: G 180 ARG cc_start: 0.8276 (mtt180) cc_final: 0.7694 (mmt-90) REVERT: G 227 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8888 (ttm-80) REVERT: G 291 ASP cc_start: 0.8428 (m-30) cc_final: 0.8206 (m-30) REVERT: G 308 LYS cc_start: 0.8944 (mttt) cc_final: 0.8620 (mttm) REVERT: G 355 ASN cc_start: 0.8523 (p0) cc_final: 0.8301 (p0) REVERT: G 369 TRP cc_start: 0.9150 (t60) cc_final: 0.8772 (t60) REVERT: G 499 HIS cc_start: 0.8468 (m-70) cc_final: 0.7986 (p-80) REVERT: G 526 ASP cc_start: 0.8980 (t70) cc_final: 0.8313 (t70) REVERT: G 534 TYR cc_start: 0.9002 (t80) cc_final: 0.7895 (t80) REVERT: H 9 GLN cc_start: 0.8886 (mp10) cc_final: 0.8628 (pm20) REVERT: H 12 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8421 (mm-30) REVERT: H 14 LYS cc_start: 0.8815 (tptp) cc_final: 0.8544 (tppt) REVERT: H 37 MET cc_start: 0.9440 (mmm) cc_final: 0.9148 (mmm) REVERT: H 52 MET cc_start: 0.9202 (mtm) cc_final: 0.8782 (mtm) REVERT: H 54 ASN cc_start: 0.9274 (m-40) cc_final: 0.8811 (m110) REVERT: H 72 MET cc_start: 0.9493 (OUTLIER) cc_final: 0.8992 (tmm) REVERT: H 91 ARG cc_start: 0.8662 (ttm170) cc_final: 0.8401 (ttm110) REVERT: H 115 GLU cc_start: 0.8752 (mp0) cc_final: 0.8342 (mp0) REVERT: H 117 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8373 (mt) REVERT: H 121 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8420 (mm-30) REVERT: H 125 MET cc_start: 0.9497 (ttt) cc_final: 0.9163 (ttt) outliers start: 71 outliers final: 35 residues processed: 663 average time/residue: 0.1080 time to fit residues: 109.4344 Evaluate side-chains 669 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 620 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 498 HIS Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 110 TRP Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 498 HIS Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 498 HIS Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 7 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 179 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.091839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.075456 restraints weight = 38635.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.078226 restraints weight = 19642.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.080132 restraints weight = 12384.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.081510 restraints weight = 8811.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.082462 restraints weight = 6805.751| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15228 Z= 0.152 Angle : 0.619 10.604 20644 Z= 0.310 Chirality : 0.038 0.177 2368 Planarity : 0.003 0.034 2576 Dihedral : 3.525 18.111 2104 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.90 % Allowed : 29.07 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.36 (0.20), residues: 1904 helix: 3.01 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.16 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 127 TYR 0.024 0.002 TYR C 534 PHE 0.021 0.002 PHE E 260 TRP 0.007 0.001 TRP G 295 HIS 0.002 0.001 HIS G 230 Details of bonding type rmsd covalent geometry : bond 0.00348 (15228) covalent geometry : angle 0.61857 (20644) hydrogen bonds : bond 0.03546 ( 1112) hydrogen bonds : angle 3.90768 ( 3336) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 632 time to evaluate : 0.623 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 166 TRP cc_start: 0.8495 (t60) cc_final: 0.8018 (t60) REVERT: A 180 ARG cc_start: 0.8202 (mtt180) cc_final: 0.7659 (mmt-90) REVERT: A 227 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.7614 (ttp80) REVERT: A 291 ASP cc_start: 0.8444 (m-30) cc_final: 0.8221 (m-30) REVERT: A 308 LYS cc_start: 0.8958 (mttt) cc_final: 0.8611 (mttm) REVERT: A 369 TRP cc_start: 0.9174 (t60) cc_final: 0.8858 (t60) REVERT: A 499 HIS cc_start: 0.8477 (m-70) cc_final: 0.7988 (p-80) REVERT: A 526 ASP cc_start: 0.8998 (t70) cc_final: 0.8300 (t70) REVERT: A 533 GLN cc_start: 0.9083 (tm-30) cc_final: 0.8657 (tm-30) REVERT: A 534 TYR cc_start: 0.8977 (t80) cc_final: 0.8529 (t80) REVERT: B 9 GLN cc_start: 0.8909 (mp10) cc_final: 0.8090 (pt0) REVERT: B 12 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8437 (mm-30) REVERT: B 14 LYS cc_start: 0.8887 (tptp) cc_final: 0.8571 (tppt) REVERT: B 37 MET cc_start: 0.9441 (mmm) cc_final: 0.9150 (mmm) REVERT: B 52 MET cc_start: 0.9215 (mtm) cc_final: 0.8769 (mtm) REVERT: B 54 ASN cc_start: 0.9273 (m-40) cc_final: 0.8812 (m110) REVERT: B 72 MET cc_start: 0.9502 (OUTLIER) cc_final: 0.9021 (tmm) REVERT: B 91 ARG cc_start: 0.8595 (ttm170) cc_final: 0.8386 (ttm110) REVERT: B 112 ASN cc_start: 0.8710 (m-40) cc_final: 0.8313 (m110) REVERT: B 115 GLU cc_start: 0.8727 (mp0) cc_final: 0.8330 (mp0) REVERT: B 117 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8647 (mt) REVERT: B 120 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8686 (mm-30) REVERT: B 121 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8504 (mm-30) REVERT: B 125 MET cc_start: 0.9495 (ttt) cc_final: 0.9169 (ttt) REVERT: C 104 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.8989 (tp) REVERT: C 166 TRP cc_start: 0.8590 (t60) cc_final: 0.8068 (t60) REVERT: C 180 ARG cc_start: 0.8243 (mtt180) cc_final: 0.7580 (mtt-85) REVERT: C 229 LEU cc_start: 0.9787 (mt) cc_final: 0.9584 (mm) REVERT: C 291 ASP cc_start: 0.8442 (m-30) cc_final: 0.8223 (m-30) REVERT: C 308 LYS cc_start: 0.8952 (mttt) cc_final: 0.8612 (mttm) REVERT: C 355 ASN cc_start: 0.8528 (p0) cc_final: 0.8312 (p0) REVERT: C 369 TRP cc_start: 0.9179 (t60) cc_final: 0.8858 (t60) REVERT: C 499 HIS cc_start: 0.8473 (m-70) cc_final: 0.7987 (p-80) REVERT: C 526 ASP cc_start: 0.9025 (t70) cc_final: 0.8366 (t70) REVERT: D 9 GLN cc_start: 0.8910 (mp10) cc_final: 0.8092 (pt0) REVERT: D 12 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8434 (mm-30) REVERT: D 14 LYS cc_start: 0.8889 (tptp) cc_final: 0.8572 (tppt) REVERT: D 37 MET cc_start: 0.9441 (mmm) cc_final: 0.9150 (mmm) REVERT: D 52 MET cc_start: 0.9222 (mtm) cc_final: 0.8771 (mtm) REVERT: D 54 ASN cc_start: 0.9270 (m-40) cc_final: 0.8807 (m110) REVERT: D 72 MET cc_start: 0.9486 (OUTLIER) cc_final: 0.9017 (tmm) REVERT: D 112 ASN cc_start: 0.8643 (m-40) cc_final: 0.8157 (m110) REVERT: D 115 GLU cc_start: 0.8749 (mp0) cc_final: 0.8338 (mp0) REVERT: D 117 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8638 (mt) REVERT: D 120 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8688 (mm-30) REVERT: D 121 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8507 (mm-30) REVERT: D 124 GLU cc_start: 0.9168 (tp30) cc_final: 0.8951 (tp30) REVERT: D 125 MET cc_start: 0.9488 (ttt) cc_final: 0.9163 (ttt) REVERT: E 166 TRP cc_start: 0.8498 (t60) cc_final: 0.8025 (t60) REVERT: E 180 ARG cc_start: 0.8245 (mtt180) cc_final: 0.7705 (mmt-90) REVERT: E 227 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.7593 (ttp80) REVERT: E 291 ASP cc_start: 0.8442 (m-30) cc_final: 0.8221 (m-30) REVERT: E 308 LYS cc_start: 0.8965 (mttt) cc_final: 0.8614 (mttm) REVERT: E 369 TRP cc_start: 0.9174 (t60) cc_final: 0.8863 (t60) REVERT: E 499 HIS cc_start: 0.8474 (m-70) cc_final: 0.7986 (p-80) REVERT: E 526 ASP cc_start: 0.9003 (t70) cc_final: 0.8316 (t70) REVERT: E 534 TYR cc_start: 0.9004 (t80) cc_final: 0.8505 (t80) REVERT: F 9 GLN cc_start: 0.8908 (mp10) cc_final: 0.8088 (pt0) REVERT: F 12 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8444 (mm-30) REVERT: F 14 LYS cc_start: 0.8887 (tptp) cc_final: 0.8571 (tppt) REVERT: F 37 MET cc_start: 0.9444 (mmm) cc_final: 0.9155 (mmm) REVERT: F 52 MET cc_start: 0.9221 (mtm) cc_final: 0.8771 (mtm) REVERT: F 54 ASN cc_start: 0.9219 (m-40) cc_final: 0.8758 (m110) REVERT: F 72 MET cc_start: 0.9488 (OUTLIER) cc_final: 0.9017 (tmm) REVERT: F 112 ASN cc_start: 0.8714 (m-40) cc_final: 0.8316 (m110) REVERT: F 115 GLU cc_start: 0.8726 (mp0) cc_final: 0.7994 (mp0) REVERT: F 117 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8644 (mt) REVERT: F 120 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8696 (mm-30) REVERT: F 121 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8498 (mm-30) REVERT: F 125 MET cc_start: 0.9496 (ttt) cc_final: 0.9171 (ttt) REVERT: G 104 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8980 (tp) REVERT: G 166 TRP cc_start: 0.8594 (t60) cc_final: 0.8071 (t60) REVERT: G 180 ARG cc_start: 0.8243 (mtt180) cc_final: 0.7578 (mtt-85) REVERT: G 227 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.7624 (ttp80) REVERT: G 291 ASP cc_start: 0.8443 (m-30) cc_final: 0.8224 (m-30) REVERT: G 308 LYS cc_start: 0.8956 (mttt) cc_final: 0.8617 (mttm) REVERT: G 369 TRP cc_start: 0.9182 (t60) cc_final: 0.8863 (t60) REVERT: G 499 HIS cc_start: 0.8471 (m-70) cc_final: 0.7986 (p-80) REVERT: G 526 ASP cc_start: 0.8989 (t70) cc_final: 0.8300 (t70) REVERT: G 534 TYR cc_start: 0.8822 (t80) cc_final: 0.7504 (t80) REVERT: H 9 GLN cc_start: 0.8908 (mp10) cc_final: 0.8084 (pt0) REVERT: H 12 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8427 (mm-30) REVERT: H 14 LYS cc_start: 0.8894 (tptp) cc_final: 0.8576 (tppt) REVERT: H 37 MET cc_start: 0.9443 (mmm) cc_final: 0.9152 (mmm) REVERT: H 52 MET cc_start: 0.9221 (mtm) cc_final: 0.8771 (mtm) REVERT: H 54 ASN cc_start: 0.9273 (m-40) cc_final: 0.8827 (m110) REVERT: H 72 MET cc_start: 0.9493 (OUTLIER) cc_final: 0.9017 (tmm) REVERT: H 115 GLU cc_start: 0.8756 (mp0) cc_final: 0.8345 (mp0) REVERT: H 117 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8641 (mt) REVERT: H 120 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8697 (mm-30) REVERT: H 121 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8497 (mm-30) REVERT: H 125 MET cc_start: 0.9490 (ttt) cc_final: 0.9170 (ttt) outliers start: 71 outliers final: 45 residues processed: 655 average time/residue: 0.1091 time to fit residues: 109.1502 Evaluate side-chains 678 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 620 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 498 HIS Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 110 TRP Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 498 HIS Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 498 HIS Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 91 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 119 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.093821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.076868 restraints weight = 38179.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.079674 restraints weight = 19437.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.081621 restraints weight = 12336.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.083031 restraints weight = 8847.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.084048 restraints weight = 6869.527| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15228 Z= 0.139 Angle : 0.636 11.238 20644 Z= 0.316 Chirality : 0.039 0.184 2368 Planarity : 0.004 0.053 2576 Dihedral : 3.495 18.254 2104 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.49 % Allowed : 29.97 % Favored : 65.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.27 (0.20), residues: 1904 helix: 2.92 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.10 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 127 TYR 0.023 0.001 TYR C 534 PHE 0.026 0.002 PHE G 341 TRP 0.008 0.001 TRP A 295 HIS 0.003 0.001 HIS F 108 Details of bonding type rmsd covalent geometry : bond 0.00325 (15228) covalent geometry : angle 0.63614 (20644) hydrogen bonds : bond 0.03553 ( 1112) hydrogen bonds : angle 3.91557 ( 3336) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 643 time to evaluate : 0.580 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 166 TRP cc_start: 0.8366 (t60) cc_final: 0.7895 (t60) REVERT: A 180 ARG cc_start: 0.8224 (mtt180) cc_final: 0.7656 (mmt-90) REVERT: A 227 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8800 (ttm-80) REVERT: A 291 ASP cc_start: 0.8419 (m-30) cc_final: 0.8204 (m-30) REVERT: A 308 LYS cc_start: 0.8933 (mttt) cc_final: 0.8597 (mttm) REVERT: A 369 TRP cc_start: 0.9114 (t60) cc_final: 0.8857 (t60) REVERT: A 499 HIS cc_start: 0.8467 (m-70) cc_final: 0.7982 (p-80) REVERT: A 526 ASP cc_start: 0.8986 (t70) cc_final: 0.8297 (t70) REVERT: A 533 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8521 (tm-30) REVERT: A 534 TYR cc_start: 0.8859 (t80) cc_final: 0.8460 (t80) REVERT: B 9 GLN cc_start: 0.8894 (mp10) cc_final: 0.8113 (pt0) REVERT: B 12 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8472 (mm-30) REVERT: B 14 LYS cc_start: 0.8827 (tptp) cc_final: 0.8522 (tppt) REVERT: B 37 MET cc_start: 0.9416 (mmm) cc_final: 0.9130 (mmm) REVERT: B 50 GLN cc_start: 0.9315 (tp40) cc_final: 0.9036 (tp40) REVERT: B 52 MET cc_start: 0.9210 (mtm) cc_final: 0.8750 (mtm) REVERT: B 54 ASN cc_start: 0.9210 (m-40) cc_final: 0.8745 (m110) REVERT: B 72 MET cc_start: 0.9482 (OUTLIER) cc_final: 0.8990 (tmm) REVERT: B 112 ASN cc_start: 0.8668 (m-40) cc_final: 0.8265 (m110) REVERT: B 115 GLU cc_start: 0.8730 (mp0) cc_final: 0.8329 (mp0) REVERT: B 117 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8376 (mt) REVERT: B 119 ASP cc_start: 0.8814 (p0) cc_final: 0.8593 (p0) REVERT: B 120 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8612 (mm-30) REVERT: B 121 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8463 (mm-30) REVERT: B 125 MET cc_start: 0.9548 (ttt) cc_final: 0.9227 (ttt) REVERT: C 104 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8935 (tp) REVERT: C 166 TRP cc_start: 0.8508 (t60) cc_final: 0.7974 (t60) REVERT: C 180 ARG cc_start: 0.8221 (mtt180) cc_final: 0.7534 (mtt-85) REVERT: C 291 ASP cc_start: 0.8417 (m-30) cc_final: 0.8215 (m-30) REVERT: C 308 LYS cc_start: 0.8913 (mttt) cc_final: 0.8579 (mttm) REVERT: C 355 ASN cc_start: 0.8463 (p0) cc_final: 0.8220 (p0) REVERT: C 369 TRP cc_start: 0.9124 (t60) cc_final: 0.8859 (t60) REVERT: C 499 HIS cc_start: 0.8466 (m-70) cc_final: 0.7982 (p-80) REVERT: C 526 ASP cc_start: 0.9005 (t70) cc_final: 0.8119 (t70) REVERT: D 9 GLN cc_start: 0.8899 (mp10) cc_final: 0.8120 (pt0) REVERT: D 12 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8472 (mm-30) REVERT: D 14 LYS cc_start: 0.8829 (tptp) cc_final: 0.8521 (tppt) REVERT: D 37 MET cc_start: 0.9412 (mmm) cc_final: 0.9129 (mmm) REVERT: D 50 GLN cc_start: 0.9304 (tp40) cc_final: 0.9027 (tp40) REVERT: D 52 MET cc_start: 0.9218 (mtm) cc_final: 0.8748 (mtm) REVERT: D 54 ASN cc_start: 0.9200 (m-40) cc_final: 0.8735 (m110) REVERT: D 72 MET cc_start: 0.9475 (OUTLIER) cc_final: 0.8989 (tmm) REVERT: D 112 ASN cc_start: 0.8566 (m-40) cc_final: 0.8066 (m110) REVERT: D 115 GLU cc_start: 0.8756 (mp0) cc_final: 0.8340 (mp0) REVERT: D 117 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8362 (mt) REVERT: D 119 ASP cc_start: 0.8806 (p0) cc_final: 0.8586 (p0) REVERT: D 120 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8610 (mm-30) REVERT: D 121 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8474 (mm-30) REVERT: D 124 GLU cc_start: 0.9178 (tp30) cc_final: 0.8962 (tp30) REVERT: D 125 MET cc_start: 0.9515 (ttt) cc_final: 0.9184 (ttt) REVERT: E 133 SER cc_start: 0.8854 (t) cc_final: 0.8435 (p) REVERT: E 166 TRP cc_start: 0.8374 (t60) cc_final: 0.7908 (t60) REVERT: E 180 ARG cc_start: 0.8226 (mtt180) cc_final: 0.7658 (mmt-90) REVERT: E 227 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8798 (ttm-80) REVERT: E 291 ASP cc_start: 0.8423 (m-30) cc_final: 0.8208 (m-30) REVERT: E 308 LYS cc_start: 0.8941 (mttt) cc_final: 0.8602 (mttm) REVERT: E 369 TRP cc_start: 0.9109 (t60) cc_final: 0.8859 (t60) REVERT: E 499 HIS cc_start: 0.8465 (m-70) cc_final: 0.7982 (p-80) REVERT: E 526 ASP cc_start: 0.8998 (t70) cc_final: 0.8160 (t70) REVERT: F 9 GLN cc_start: 0.8895 (mp10) cc_final: 0.8111 (pt0) REVERT: F 12 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8475 (mm-30) REVERT: F 14 LYS cc_start: 0.8823 (tptp) cc_final: 0.8517 (tppt) REVERT: F 37 MET cc_start: 0.9415 (mmm) cc_final: 0.9132 (mmm) REVERT: F 50 GLN cc_start: 0.9311 (tp40) cc_final: 0.9031 (tp40) REVERT: F 52 MET cc_start: 0.9215 (mtm) cc_final: 0.8751 (mtm) REVERT: F 54 ASN cc_start: 0.9203 (m-40) cc_final: 0.8734 (m110) REVERT: F 72 MET cc_start: 0.9481 (OUTLIER) cc_final: 0.8991 (tmm) REVERT: F 112 ASN cc_start: 0.8669 (m-40) cc_final: 0.8267 (m110) REVERT: F 115 GLU cc_start: 0.8733 (mp0) cc_final: 0.8333 (mp0) REVERT: F 117 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8377 (mt) REVERT: F 119 ASP cc_start: 0.8809 (p0) cc_final: 0.8588 (p0) REVERT: F 120 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8609 (mm-30) REVERT: F 121 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8456 (mm-30) REVERT: F 125 MET cc_start: 0.9549 (ttt) cc_final: 0.9228 (ttt) REVERT: G 104 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8931 (tp) REVERT: G 166 TRP cc_start: 0.8510 (t60) cc_final: 0.7978 (t60) REVERT: G 180 ARG cc_start: 0.8223 (mtt180) cc_final: 0.7535 (mtt-85) REVERT: G 227 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.7381 (ttp80) REVERT: G 291 ASP cc_start: 0.8422 (m-30) cc_final: 0.8220 (m-30) REVERT: G 308 LYS cc_start: 0.8918 (mttt) cc_final: 0.8583 (mttm) REVERT: G 369 TRP cc_start: 0.9127 (t60) cc_final: 0.8861 (t60) REVERT: G 499 HIS cc_start: 0.8464 (m-70) cc_final: 0.7982 (p-80) REVERT: G 526 ASP cc_start: 0.8976 (t70) cc_final: 0.8084 (t70) REVERT: G 534 TYR cc_start: 0.8561 (t80) cc_final: 0.7502 (t80) REVERT: H 9 GLN cc_start: 0.8896 (mp10) cc_final: 0.8111 (pt0) REVERT: H 12 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8461 (mm-30) REVERT: H 14 LYS cc_start: 0.8835 (tptp) cc_final: 0.8527 (tppt) REVERT: H 37 MET cc_start: 0.9420 (mmm) cc_final: 0.9132 (mmm) REVERT: H 50 GLN cc_start: 0.9311 (tp40) cc_final: 0.9035 (tp40) REVERT: H 52 MET cc_start: 0.9214 (mtm) cc_final: 0.8748 (mtm) REVERT: H 54 ASN cc_start: 0.9204 (m-40) cc_final: 0.8737 (m110) REVERT: H 72 MET cc_start: 0.9473 (OUTLIER) cc_final: 0.8988 (tmm) REVERT: H 115 GLU cc_start: 0.8734 (mp0) cc_final: 0.8330 (mp0) REVERT: H 117 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8349 (mt) REVERT: H 119 ASP cc_start: 0.8811 (p0) cc_final: 0.8589 (p0) REVERT: H 120 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8610 (mm-30) REVERT: H 121 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8459 (mm-30) REVERT: H 125 MET cc_start: 0.9550 (ttt) cc_final: 0.9227 (ttt) outliers start: 65 outliers final: 37 residues processed: 656 average time/residue: 0.1097 time to fit residues: 110.4792 Evaluate side-chains 676 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 626 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 110 TRP Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 371 CYS Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 108 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 171 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.091305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.075112 restraints weight = 38744.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.077790 restraints weight = 19696.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.079653 restraints weight = 12439.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.080992 restraints weight = 8873.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.081825 restraints weight = 6866.704| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15228 Z= 0.176 Angle : 0.649 11.059 20644 Z= 0.325 Chirality : 0.039 0.191 2368 Planarity : 0.004 0.058 2576 Dihedral : 3.506 18.514 2104 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.94 % Allowed : 30.80 % Favored : 65.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.29 (0.20), residues: 1904 helix: 2.92 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.04 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 127 TYR 0.026 0.002 TYR C 534 PHE 0.027 0.002 PHE A 341 TRP 0.006 0.001 TRP G 295 HIS 0.003 0.001 HIS H 108 Details of bonding type rmsd covalent geometry : bond 0.00402 (15228) covalent geometry : angle 0.64874 (20644) hydrogen bonds : bond 0.03596 ( 1112) hydrogen bonds : angle 4.03253 ( 3336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2877.75 seconds wall clock time: 50 minutes 16.82 seconds (3016.82 seconds total)