Starting phenix.real_space_refine on Sat Sep 12 09:16:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5vms_8712/09_2026/5vms_8712.cif Found real_map, /net/cci-nas-00/data/ceres_data/5vms_8712/09_2026/5vms_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_8712/09_2026/5vms_8712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5vms_8712/09_2026/5vms_8712.map" restraint_files = "/net/cci-nas-00/data/ceres_data/5vms_8712/09_2026/5vms_8712.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5vms_8712/09_2026/5vms_8712.cif" model { file = "/net/cci-nas-00/data/ceres_data/5vms_8712/09_2026/5vms_8712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5vms_8712/09_2026/5vms_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 2.49, per 1000 atoms: 0.17 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: 1.28 Conformation dependent library (CDL) restraints added in 618.3 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: 0.36 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: 2.46 Time building geometry restraints manager: 1.73 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.840 Find NCS groups from input model: 0.140 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 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/Z covalent geometry : bond 0.00738 / 0.53 (15228) covalent geometry : angle 1.47399 / 1.15 (20644) hydrogen bonds : bond 0.11619 / 7.97 ( 1112) hydrogen bonds : angle 4.38215 / 3.28 ( 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 : 0.493 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: 0.8332 (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: 0.7881 (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: 0.7769 (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: 0.7881 (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: 0.9207 (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: 0.7880 (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: 0.1150 time to fit residues: 155.0093 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 : 0.583 ------------------------------------------------------------------------------- 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... A 357 GLN A 366 GLN B 112 ASN C 357 GLN C 366 GLN D 112 ASN E 357 GLN E 366 GLN F 112 ASN G 357 GLN G 366 GLN H 112 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.093307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.076244 restraints weight = 37102.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.079146 restraints weight = 18885.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.081200 restraints weight = 11830.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.082667 restraints weight = 8376.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.083739 restraints weight = 6420.593| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 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 = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15228 Z= 0.153 Angle : 0.603 6.254 20644 Z= 0.325 Chirality : 0.041 0.224 2368 Planarity : 0.004 0.040 2576 Dihedral : 3.955 22.586 2104 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.83 % Allowed : 18.30 % Favored : 76.86 % 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: 4.03 (0.19), residues: 1904 helix: 3.72 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.69 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 75 TYR 0.019 0.002 TYR C 534 PHE 0.025 0.002 PHE D 17 TRP 0.013 0.001 TRP A 369 HIS 0.006 0.001 HIS D 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (15228) covalent geometry : angle 0.60273 / 0.32 (20644) hydrogen bonds : bond 0.04217 / 2.88 ( 1112) hydrogen bonds : angle 3.95251 / 2.97 ( 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 763 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 693 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.8541 (t60) cc_final: 0.8153 (t60) REVERT: A 180 ARG cc_start: 0.8334 (mtt180) cc_final: 0.7873 (mpt-90) REVERT: A 291 ASP cc_start: 0.8503 (m-30) cc_final: 0.8126 (m-30) REVERT: A 308 LYS cc_start: 0.9037 (mttt) cc_final: 0.8502 (mttm) REVERT: A 384 ILE cc_start: 0.8114 (mp) cc_final: 0.7877 (mt) REVERT: A 499 HIS cc_start: 0.8528 (m-70) cc_final: 0.8020 (p-80) REVERT: A 522 ARG cc_start: 0.9013 (tpp80) cc_final: 0.8765 (mmm-85) REVERT: A 526 ASP cc_start: 0.8865 (t70) cc_final: 0.8179 (t70) REVERT: A 534 TYR cc_start: 0.9093 (t80) cc_final: 0.8636 (t80) REVERT: A 536 GLN cc_start: 0.9554 (tt0) cc_final: 0.9324 (tt0) REVERT: A 551 ARG cc_start: 0.8871 (tpp-160) cc_final: 0.8500 (tpt170) REVERT: B 9 GLN cc_start: 0.8781 (mp10) cc_final: 0.8332 (pt0) REVERT: B 10 ILE cc_start: 0.9008 (tt) cc_final: 0.8779 (mt) REVERT: B 52 MET cc_start: 0.9153 (mtm) cc_final: 0.8907 (mtp) REVERT: B 115 GLU cc_start: 0.8514 (mp0) cc_final: 0.8201 (mp0) REVERT: B 117 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8708 (mt) REVERT: B 121 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8285 (mm-30) REVERT: B 124 GLU cc_start: 0.9070 (tp30) cc_final: 0.8795 (tp30) REVERT: B 125 MET cc_start: 0.9483 (ttt) cc_final: 0.9239 (ttp) REVERT: B 127 ARG cc_start: 0.9166 (ttp-110) cc_final: 0.8873 (ttm110) REVERT: B 142 PHE cc_start: 0.8951 (t80) cc_final: 0.8731 (t80) REVERT: C 166 TRP cc_start: 0.8534 (t60) cc_final: 0.8147 (t60) REVERT: C 180 ARG cc_start: 0.8333 (mtt180) cc_final: 0.7864 (mpt-90) REVERT: C 291 ASP cc_start: 0.8509 (m-30) cc_final: 0.8127 (m-30) REVERT: C 308 LYS cc_start: 0.9039 (mttt) cc_final: 0.8507 (mttm) REVERT: C 384 ILE cc_start: 0.8115 (mp) cc_final: 0.7880 (mt) REVERT: C 499 HIS cc_start: 0.8526 (m-70) cc_final: 0.8018 (p-80) REVERT: C 522 ARG cc_start: 0.9011 (tpp80) cc_final: 0.8764 (mmm-85) REVERT: C 526 ASP cc_start: 0.8862 (t70) cc_final: 0.8176 (t70) REVERT: C 534 TYR cc_start: 0.9095 (t80) cc_final: 0.8637 (t80) REVERT: C 536 GLN cc_start: 0.9552 (tt0) cc_final: 0.9325 (tt0) REVERT: D 9 GLN cc_start: 0.8781 (mp10) cc_final: 0.8330 (pt0) REVERT: D 10 ILE cc_start: 0.9009 (tt) cc_final: 0.8782 (mt) REVERT: D 52 MET cc_start: 0.9155 (mtm) cc_final: 0.8907 (mtp) REVERT: D 115 GLU cc_start: 0.8518 (mp0) cc_final: 0.8205 (mp0) REVERT: D 117 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8708 (mt) REVERT: D 121 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8285 (mm-30) REVERT: D 124 GLU cc_start: 0.9073 (tp30) cc_final: 0.8798 (tp30) REVERT: D 125 MET cc_start: 0.9480 (ttt) cc_final: 0.9238 (ttp) REVERT: D 127 ARG cc_start: 0.9164 (ttp-110) cc_final: 0.8870 (ttm110) REVERT: D 142 PHE cc_start: 0.8954 (t80) cc_final: 0.8734 (t80) REVERT: E 166 TRP cc_start: 0.8547 (t60) cc_final: 0.8161 (t60) REVERT: E 180 ARG cc_start: 0.8335 (mtt180) cc_final: 0.7874 (mpt-90) REVERT: E 291 ASP cc_start: 0.8509 (m-30) cc_final: 0.8129 (m-30) REVERT: E 308 LYS cc_start: 0.9040 (mttt) cc_final: 0.8504 (mttm) REVERT: E 384 ILE cc_start: 0.8115 (mp) cc_final: 0.7882 (mt) REVERT: E 499 HIS cc_start: 0.8526 (m-70) cc_final: 0.8017 (p-80) REVERT: E 522 ARG cc_start: 0.9011 (tpp80) cc_final: 0.8764 (mmm-85) REVERT: E 526 ASP cc_start: 0.8864 (t70) cc_final: 0.8179 (t70) REVERT: E 534 TYR cc_start: 0.9094 (t80) cc_final: 0.8636 (t80) REVERT: E 536 GLN cc_start: 0.9552 (tt0) cc_final: 0.9323 (tt0) REVERT: E 550 ARG cc_start: 0.9056 (ttm110) cc_final: 0.8847 (mtm110) REVERT: F 9 GLN cc_start: 0.8778 (mp10) cc_final: 0.8329 (pt0) REVERT: F 10 ILE cc_start: 0.9014 (tt) cc_final: 0.8783 (mt) REVERT: F 52 MET cc_start: 0.9149 (mtm) cc_final: 0.8909 (mtp) REVERT: F 115 GLU cc_start: 0.8517 (mp0) cc_final: 0.8204 (mp0) REVERT: F 117 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8707 (mt) REVERT: F 121 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8287 (mm-30) REVERT: F 124 GLU cc_start: 0.9072 (tp30) cc_final: 0.8798 (tp30) REVERT: F 125 MET cc_start: 0.9483 (ttt) cc_final: 0.9241 (ttp) REVERT: F 127 ARG cc_start: 0.9163 (ttp-110) cc_final: 0.8872 (ttm110) REVERT: F 142 PHE cc_start: 0.8951 (t80) cc_final: 0.8731 (t80) REVERT: G 166 TRP cc_start: 0.8538 (t60) cc_final: 0.8153 (t60) REVERT: G 180 ARG cc_start: 0.8332 (mtt180) cc_final: 0.7864 (mpt-90) REVERT: G 291 ASP cc_start: 0.8505 (m-30) cc_final: 0.8123 (m-30) REVERT: G 308 LYS cc_start: 0.9038 (mttt) cc_final: 0.8503 (mttm) REVERT: G 384 ILE cc_start: 0.8113 (mp) cc_final: 0.7877 (mt) REVERT: G 499 HIS cc_start: 0.8524 (m-70) cc_final: 0.8016 (p-80) REVERT: G 522 ARG cc_start: 0.9015 (tpp80) cc_final: 0.8767 (mmm-85) REVERT: G 526 ASP cc_start: 0.8864 (t70) cc_final: 0.8177 (t70) REVERT: G 534 TYR cc_start: 0.9094 (t80) cc_final: 0.8634 (t80) REVERT: G 536 GLN cc_start: 0.9556 (tt0) cc_final: 0.9326 (tt0) REVERT: G 549 GLN cc_start: 0.9386 (tp40) cc_final: 0.9024 (tp40) REVERT: H 9 GLN cc_start: 0.8778 (mp10) cc_final: 0.8329 (pt0) REVERT: H 10 ILE cc_start: 0.9005 (tt) cc_final: 0.8777 (mt) REVERT: H 52 MET cc_start: 0.9152 (mtm) cc_final: 0.8910 (mtp) REVERT: H 115 GLU cc_start: 0.8515 (mp0) cc_final: 0.8202 (mp0) REVERT: H 117 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8707 (mt) REVERT: H 121 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8287 (mm-30) REVERT: H 124 GLU cc_start: 0.9071 (tp30) cc_final: 0.8795 (tp30) REVERT: H 125 MET cc_start: 0.9482 (ttt) cc_final: 0.9238 (ttp) REVERT: H 127 ARG cc_start: 0.9166 (ttp-110) cc_final: 0.8874 (ttm110) REVERT: H 142 PHE cc_start: 0.8948 (t80) cc_final: 0.8730 (t80) outliers start: 70 outliers final: 48 residues processed: 719 average time/residue: 0.1097 time to fit residues: 120.8662 Evaluate side-chains 698 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 646 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 345 VAL 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 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 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 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: 0.2980 chunk 140 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 181 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 54 ASN B 112 ASN D 54 ASN D 112 ASN F 54 ASN F 112 ASN H 54 ASN H 112 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.089596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.072829 restraints weight = 39143.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.075536 restraints weight = 19973.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.077462 restraints weight = 12673.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.078795 restraints weight = 9075.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.079753 restraints weight = 7084.345| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15228 Z= 0.219 Angle : 0.585 5.947 20644 Z= 0.321 Chirality : 0.041 0.140 2368 Planarity : 0.004 0.032 2576 Dihedral : 3.933 22.428 2104 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 7.73 % Allowed : 18.78 % Favored : 73.48 % 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: 3.66 (0.20), residues: 1904 helix: 3.36 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.39 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 227 TYR 0.017 0.002 TYR E 268 PHE 0.019 0.002 PHE C 260 TRP 0.008 0.001 TRP G 295 HIS 0.004 0.001 HIS F 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 (15228) covalent geometry : angle 0.58470 / 0.32 (20644) hydrogen bonds : bond 0.04047 / 2.78 ( 1112) hydrogen bonds : angle 4.20990 / 3.16 ( 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 744 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 632 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.8643 (t60) cc_final: 0.8193 (t60) REVERT: A 180 ARG cc_start: 0.8278 (mtt180) cc_final: 0.7814 (mpt-90) REVERT: A 291 ASP cc_start: 0.8435 (m-30) cc_final: 0.8108 (m-30) REVERT: A 307 ASP cc_start: 0.8946 (p0) cc_final: 0.8714 (p0) REVERT: A 308 LYS cc_start: 0.9147 (mttt) cc_final: 0.8639 (mttm) REVERT: A 355 ASN cc_start: 0.8420 (p0) cc_final: 0.8143 (p0) REVERT: A 369 TRP cc_start: 0.9071 (t60) cc_final: 0.8825 (t60) REVERT: A 499 HIS cc_start: 0.8542 (m-70) cc_final: 0.8131 (p-80) REVERT: A 526 ASP cc_start: 0.8976 (t70) cc_final: 0.8356 (t70) REVERT: B 9 GLN cc_start: 0.8737 (mp10) cc_final: 0.8286 (pt0) REVERT: B 37 MET cc_start: 0.9464 (mmm) cc_final: 0.9174 (mmm) REVERT: B 46 GLU cc_start: 0.9132 (tp30) cc_final: 0.8915 (tp30) REVERT: B 52 MET cc_start: 0.9237 (mtm) cc_final: 0.8793 (mtp) REVERT: B 54 ASN cc_start: 0.9107 (m-40) cc_final: 0.8775 (m110) REVERT: B 72 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8704 (mtm) REVERT: B 77 MET cc_start: 0.8407 (mmm) cc_final: 0.8116 (mmm) REVERT: B 115 GLU cc_start: 0.8711 (mp0) cc_final: 0.8238 (mp0) REVERT: B 117 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8717 (mt) REVERT: B 119 ASP cc_start: 0.9010 (p0) cc_final: 0.8632 (p0) REVERT: B 120 GLU cc_start: 0.9081 (tp30) cc_final: 0.8663 (mm-30) REVERT: B 121 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8157 (mm-30) REVERT: B 125 MET cc_start: 0.9488 (ttt) cc_final: 0.9161 (ttt) REVERT: C 166 TRP cc_start: 0.8676 (t60) cc_final: 0.8240 (t60) REVERT: C 180 ARG cc_start: 0.8319 (mtt180) cc_final: 0.7856 (mpt-90) REVERT: C 291 ASP cc_start: 0.8434 (m-30) cc_final: 0.8105 (m-30) REVERT: C 307 ASP cc_start: 0.8940 (p0) cc_final: 0.8715 (p0) REVERT: C 308 LYS cc_start: 0.9139 (mttt) cc_final: 0.8634 (mttm) REVERT: C 355 ASN cc_start: 0.8419 (p0) cc_final: 0.8145 (p0) REVERT: C 369 TRP cc_start: 0.9073 (t60) cc_final: 0.8817 (t60) REVERT: C 499 HIS cc_start: 0.8542 (m-70) cc_final: 0.8130 (p-80) REVERT: C 526 ASP cc_start: 0.8970 (t70) cc_final: 0.8353 (t70) REVERT: D 9 GLN cc_start: 0.8741 (mp10) cc_final: 0.8291 (pt0) REVERT: D 37 MET cc_start: 0.9472 (mmm) cc_final: 0.9183 (mmm) REVERT: D 46 GLU cc_start: 0.9131 (tp30) cc_final: 0.8917 (tp30) REVERT: D 52 MET cc_start: 0.9231 (mtm) cc_final: 0.8791 (mtp) REVERT: D 54 ASN cc_start: 0.9112 (m-40) cc_final: 0.8775 (m110) REVERT: D 72 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8704 (mtm) REVERT: D 77 MET cc_start: 0.8409 (mmm) cc_final: 0.8118 (mmm) REVERT: D 115 GLU cc_start: 0.8709 (mp0) cc_final: 0.8238 (mp0) REVERT: D 117 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8719 (mt) REVERT: D 119 ASP cc_start: 0.9000 (p0) cc_final: 0.8620 (p0) REVERT: D 120 GLU cc_start: 0.9070 (tp30) cc_final: 0.8651 (mm-30) REVERT: D 121 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8138 (mm-30) REVERT: D 125 MET cc_start: 0.9475 (ttt) cc_final: 0.9154 (ttt) REVERT: E 166 TRP cc_start: 0.8658 (t60) cc_final: 0.8208 (t60) REVERT: E 180 ARG cc_start: 0.8281 (mtt180) cc_final: 0.7820 (mpt-90) REVERT: E 291 ASP cc_start: 0.8437 (m-30) cc_final: 0.8111 (m-30) REVERT: E 307 ASP cc_start: 0.8951 (p0) cc_final: 0.8720 (p0) REVERT: E 308 LYS cc_start: 0.9147 (mttt) cc_final: 0.8639 (mttm) REVERT: E 355 ASN cc_start: 0.8421 (p0) cc_final: 0.8121 (p0) REVERT: E 369 TRP cc_start: 0.9070 (t60) cc_final: 0.8821 (t60) REVERT: E 499 HIS cc_start: 0.8543 (m-70) cc_final: 0.8132 (p-80) REVERT: E 526 ASP cc_start: 0.8976 (t70) cc_final: 0.8360 (t70) REVERT: F 9 GLN cc_start: 0.8739 (mp10) cc_final: 0.8290 (pt0) REVERT: F 37 MET cc_start: 0.9466 (mmm) cc_final: 0.9178 (mmm) REVERT: F 46 GLU cc_start: 0.9133 (tp30) cc_final: 0.8922 (tp30) REVERT: F 52 MET cc_start: 0.9230 (mtm) cc_final: 0.8788 (mtp) REVERT: F 54 ASN cc_start: 0.9112 (m-40) cc_final: 0.8777 (m110) REVERT: F 72 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8728 (mtm) REVERT: F 77 MET cc_start: 0.8353 (mmm) cc_final: 0.7995 (mmm) REVERT: F 115 GLU cc_start: 0.8713 (mp0) cc_final: 0.8241 (mp0) REVERT: F 117 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8714 (mt) REVERT: F 119 ASP cc_start: 0.9003 (p0) cc_final: 0.8625 (p0) REVERT: F 120 GLU cc_start: 0.9079 (tp30) cc_final: 0.8660 (mm-30) REVERT: F 121 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8152 (mm-30) REVERT: F 125 MET cc_start: 0.9477 (ttt) cc_final: 0.9156 (ttt) REVERT: G 166 TRP cc_start: 0.8682 (t60) cc_final: 0.8247 (t60) REVERT: G 180 ARG cc_start: 0.8323 (mtt180) cc_final: 0.7856 (mpt-90) REVERT: G 291 ASP cc_start: 0.8436 (m-30) cc_final: 0.8106 (m-30) REVERT: G 307 ASP cc_start: 0.8947 (p0) cc_final: 0.8716 (p0) REVERT: G 308 LYS cc_start: 0.9144 (mttt) cc_final: 0.8634 (mttm) REVERT: G 355 ASN cc_start: 0.8419 (p0) cc_final: 0.8116 (p0) REVERT: G 369 TRP cc_start: 0.9072 (t60) cc_final: 0.8824 (t60) REVERT: G 499 HIS cc_start: 0.8541 (m-70) cc_final: 0.8130 (p-80) REVERT: G 526 ASP cc_start: 0.8975 (t70) cc_final: 0.8355 (t70) REVERT: H 9 GLN cc_start: 0.8737 (mp10) cc_final: 0.8286 (pt0) REVERT: H 37 MET cc_start: 0.9469 (mmm) cc_final: 0.9180 (mmm) REVERT: H 46 GLU cc_start: 0.9133 (tp30) cc_final: 0.8920 (tp30) REVERT: H 52 MET cc_start: 0.9234 (mtm) cc_final: 0.8790 (mtp) REVERT: H 54 ASN cc_start: 0.9110 (m-40) cc_final: 0.8777 (m110) REVERT: H 72 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8709 (mtm) REVERT: H 77 MET cc_start: 0.8407 (mmm) cc_final: 0.8118 (mmm) REVERT: H 115 GLU cc_start: 0.8709 (mp0) cc_final: 0.8239 (mp0) REVERT: H 117 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8715 (mt) REVERT: H 119 ASP cc_start: 0.9008 (p0) cc_final: 0.8626 (p0) REVERT: H 120 GLU cc_start: 0.9075 (tp30) cc_final: 0.8657 (mm-30) REVERT: H 121 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8149 (mm-30) REVERT: H 125 MET cc_start: 0.9477 (ttt) cc_final: 0.9156 (ttt) outliers start: 112 outliers final: 82 residues processed: 668 average time/residue: 0.1049 time to fit residues: 109.1113 Evaluate side-chains 705 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 615 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 167 SER 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 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 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 C residue 110 TRP 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 153 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 167 SER 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 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 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 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 167 SER 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 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 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 110 TRP 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 153 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 167 SER 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 41 optimal weight: 8.9990 chunk 117 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 151 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3269 r_free = 0.3269 target = 0.090469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.073744 restraints weight = 38638.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.076515 restraints weight = 19508.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.078403 restraints weight = 12260.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.079777 restraints weight = 8780.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.080688 restraints weight = 6808.430| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15228 Z= 0.161 Angle : 0.563 7.284 20644 Z= 0.296 Chirality : 0.039 0.207 2368 Planarity : 0.003 0.026 2576 Dihedral : 3.803 21.079 2104 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 6.28 % Allowed : 24.31 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.71 (0.20), residues: 1904 helix: 3.35 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.16 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 91 TYR 0.019 0.002 TYR E 268 PHE 0.019 0.002 PHE E 260 TRP 0.007 0.001 TRP G 295 HIS 0.005 0.001 HIS H 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (15228) covalent geometry : angle 0.56336 / 0.30 (20644) hydrogen bonds : bond 0.03862 / 2.64 ( 1112) hydrogen bonds : angle 4.02883 / 3.02 ( 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 743 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 652 time to evaluate : 0.587 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: 0.8633 (t60) cc_final: 0.8191 (t60) REVERT: A 180 ARG cc_start: 0.8252 (mtt180) cc_final: 0.7705 (mtt-85) REVERT: A 227 ARG cc_start: 0.9273 (OUTLIER) cc_final: 0.7756 (ttp80) REVERT: A 240 LEU cc_start: 0.9203 (tt) cc_final: 0.8579 (tt) REVERT: A 291 ASP cc_start: 0.8424 (m-30) cc_final: 0.8141 (m-30) REVERT: A 308 LYS cc_start: 0.9081 (mttt) cc_final: 0.8753 (mttm) REVERT: A 355 ASN cc_start: 0.8509 (p0) cc_final: 0.8179 (p0) REVERT: A 369 TRP cc_start: 0.9111 (t60) cc_final: 0.8858 (t60) REVERT: A 499 HIS cc_start: 0.8552 (m-70) cc_final: 0.8139 (p-80) REVERT: A 526 ASP cc_start: 0.8967 (t70) cc_final: 0.8341 (t70) REVERT: A 533 GLN cc_start: 0.9333 (tm-30) cc_final: 0.8775 (tm-30) REVERT: A 534 TYR cc_start: 0.9289 (t80) cc_final: 0.8926 (t80) REVERT: B 9 GLN cc_start: 0.8815 (mp10) cc_final: 0.8380 (pt0) REVERT: B 12 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8378 (mm-30) REVERT: B 37 MET cc_start: 0.9512 (mmm) cc_final: 0.9293 (mmm) REVERT: B 46 GLU cc_start: 0.9061 (tp30) cc_final: 0.8833 (tp30) REVERT: B 52 MET cc_start: 0.9214 (mtm) cc_final: 0.8863 (mtp) REVERT: B 54 ASN cc_start: 0.9273 (m-40) cc_final: 0.8915 (m110) REVERT: B 115 GLU cc_start: 0.8695 (mp0) cc_final: 0.8148 (mp0) REVERT: B 117 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8803 (mt) REVERT: B 119 ASP cc_start: 0.9013 (p0) cc_final: 0.8713 (p0) REVERT: B 120 GLU cc_start: 0.9072 (tp30) cc_final: 0.8720 (mm-30) REVERT: B 125 MET cc_start: 0.9487 (ttt) cc_final: 0.9161 (ttt) REVERT: C 104 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9122 (tp) REVERT: C 166 TRP cc_start: 0.8670 (t60) cc_final: 0.8201 (t60) REVERT: C 180 ARG cc_start: 0.8273 (mtt180) cc_final: 0.7722 (mtt-85) REVERT: C 227 ARG cc_start: 0.9269 (OUTLIER) cc_final: 0.7747 (ttp80) REVERT: C 240 LEU cc_start: 0.9207 (tt) cc_final: 0.8576 (tt) REVERT: C 291 ASP cc_start: 0.8424 (m-30) cc_final: 0.8141 (m-30) REVERT: C 308 LYS cc_start: 0.9072 (mttt) cc_final: 0.8745 (mttm) REVERT: C 343 LEU cc_start: 0.9085 (mt) cc_final: 0.8698 (mp) REVERT: C 355 ASN cc_start: 0.8509 (p0) cc_final: 0.8192 (p0) REVERT: C 369 TRP cc_start: 0.9113 (t60) cc_final: 0.8853 (t60) REVERT: C 499 HIS cc_start: 0.8553 (m-70) cc_final: 0.8139 (p-80) REVERT: C 526 ASP cc_start: 0.8966 (t70) cc_final: 0.8343 (t70) REVERT: C 533 GLN cc_start: 0.9339 (tm-30) cc_final: 0.8738 (tm-30) REVERT: C 534 TYR cc_start: 0.9287 (t80) cc_final: 0.8912 (t80) REVERT: D 9 GLN cc_start: 0.8813 (mp10) cc_final: 0.8378 (pt0) REVERT: D 12 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8377 (mm-30) REVERT: D 37 MET cc_start: 0.9516 (mmm) cc_final: 0.9301 (mmm) REVERT: D 46 GLU cc_start: 0.9063 (tp30) cc_final: 0.8836 (tp30) REVERT: D 52 MET cc_start: 0.9210 (mtm) cc_final: 0.8858 (mtp) REVERT: D 54 ASN cc_start: 0.9276 (m-40) cc_final: 0.8916 (m110) REVERT: D 115 GLU cc_start: 0.8695 (mp0) cc_final: 0.8149 (mp0) REVERT: D 117 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8801 (mt) REVERT: D 125 MET cc_start: 0.9483 (ttt) cc_final: 0.9160 (ttt) REVERT: E 160 GLU cc_start: 0.9243 (tt0) cc_final: 0.9021 (tt0) REVERT: E 166 TRP cc_start: 0.8639 (t60) cc_final: 0.8198 (t60) REVERT: E 180 ARG cc_start: 0.8255 (mtt180) cc_final: 0.7709 (mtt-85) REVERT: E 227 ARG cc_start: 0.9266 (OUTLIER) cc_final: 0.7746 (ttp80) REVERT: E 240 LEU cc_start: 0.9202 (tt) cc_final: 0.8569 (tt) REVERT: E 291 ASP cc_start: 0.8426 (m-30) cc_final: 0.8144 (m-30) REVERT: E 308 LYS cc_start: 0.9079 (mttt) cc_final: 0.8751 (mttm) REVERT: E 355 ASN cc_start: 0.8514 (p0) cc_final: 0.8184 (p0) REVERT: E 369 TRP cc_start: 0.9120 (t60) cc_final: 0.8856 (t60) REVERT: E 499 HIS cc_start: 0.8553 (m-70) cc_final: 0.8140 (p-80) REVERT: E 526 ASP cc_start: 0.8967 (t70) cc_final: 0.8343 (t70) REVERT: E 533 GLN cc_start: 0.9338 (tm-30) cc_final: 0.8738 (tm-30) REVERT: E 534 TYR cc_start: 0.9288 (t80) cc_final: 0.8911 (t80) REVERT: F 9 GLN cc_start: 0.8814 (mp10) cc_final: 0.8379 (pt0) REVERT: F 12 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8372 (mm-30) REVERT: F 37 MET cc_start: 0.9512 (mmm) cc_final: 0.9295 (mmm) REVERT: F 46 GLU cc_start: 0.9061 (tp30) cc_final: 0.8835 (tp30) REVERT: F 52 MET cc_start: 0.9206 (mtm) cc_final: 0.8856 (mtp) REVERT: F 54 ASN cc_start: 0.9276 (m-40) cc_final: 0.8914 (m110) REVERT: F 77 MET cc_start: 0.8423 (mmm) cc_final: 0.8083 (mmm) REVERT: F 115 GLU cc_start: 0.8697 (mp0) cc_final: 0.8149 (mp0) REVERT: F 117 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8797 (mt) REVERT: F 125 MET cc_start: 0.9484 (ttt) cc_final: 0.9160 (ttt) REVERT: G 104 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9122 (tp) REVERT: G 166 TRP cc_start: 0.8674 (t60) cc_final: 0.8205 (t60) REVERT: G 180 ARG cc_start: 0.8272 (mtt180) cc_final: 0.7722 (mtt-85) REVERT: G 227 ARG cc_start: 0.9270 (OUTLIER) cc_final: 0.7744 (ttp80) REVERT: G 240 LEU cc_start: 0.9208 (tt) cc_final: 0.8578 (tt) REVERT: G 291 ASP cc_start: 0.8425 (m-30) cc_final: 0.8140 (m-30) REVERT: G 308 LYS cc_start: 0.9078 (mttt) cc_final: 0.8750 (mttm) REVERT: G 343 LEU cc_start: 0.9084 (mt) cc_final: 0.8699 (mp) REVERT: G 355 ASN cc_start: 0.8508 (p0) cc_final: 0.8176 (p0) REVERT: G 369 TRP cc_start: 0.9114 (t60) cc_final: 0.8860 (t60) REVERT: G 499 HIS cc_start: 0.8554 (m-70) cc_final: 0.8141 (p-80) REVERT: G 526 ASP cc_start: 0.8968 (t70) cc_final: 0.8344 (t70) REVERT: G 533 GLN cc_start: 0.9336 (tm-30) cc_final: 0.8738 (tm-30) REVERT: G 534 TYR cc_start: 0.9287 (t80) cc_final: 0.8912 (t80) REVERT: H 9 GLN cc_start: 0.8813 (mp10) cc_final: 0.8378 (pt0) REVERT: H 12 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8364 (mm-30) REVERT: H 37 MET cc_start: 0.9516 (mmm) cc_final: 0.9298 (mmm) REVERT: H 46 GLU cc_start: 0.9062 (tp30) cc_final: 0.8836 (tp30) REVERT: H 52 MET cc_start: 0.9209 (mtm) cc_final: 0.8863 (mtp) REVERT: H 54 ASN cc_start: 0.9275 (m-40) cc_final: 0.8911 (m110) REVERT: H 115 GLU cc_start: 0.8694 (mp0) cc_final: 0.8147 (mp0) REVERT: H 117 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8798 (mt) REVERT: H 125 MET cc_start: 0.9484 (ttt) cc_final: 0.9160 (ttt) outliers start: 91 outliers final: 61 residues processed: 684 average time/residue: 0.1094 time to fit residues: 114.5895 Evaluate side-chains 715 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 644 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 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 513 VAL Chi-restraints excluded: chain A residue 530 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 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 118 THR Chi-restraints excluded: chain C residue 124 LEU 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 513 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain D residue 19 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 118 THR Chi-restraints excluded: chain E residue 124 LEU 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 513 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain F residue 19 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 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 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 513 VAL Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain H residue 19 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 178 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3274 r_free = 0.3274 target = 0.090937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.074472 restraints weight = 38753.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.077241 restraints weight = 19499.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.079171 restraints weight = 12267.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.080543 restraints weight = 8744.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.081341 restraints weight = 6765.383| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4057 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= 0.149 Angle : 0.574 7.843 20644 Z= 0.295 Chirality : 0.039 0.191 2368 Planarity : 0.005 0.054 2576 Dihedral : 3.710 18.658 2104 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 6.49 % Allowed : 24.59 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.68 (0.20), residues: 1904 helix: 3.26 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -0.89 (0.34), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 91 TYR 0.018 0.002 TYR A 268 PHE 0.018 0.001 PHE G 260 TRP 0.008 0.001 TRP G 295 HIS 0.005 0.001 HIS H 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (15228) covalent geometry : angle 0.57442 / 0.29 (20644) hydrogen bonds : bond 0.03711 / 2.55 ( 1112) hydrogen bonds : angle 3.92340 / 2.94 ( 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 740 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 646 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.8553 (t60) cc_final: 0.8109 (t60) REVERT: A 180 ARG cc_start: 0.8183 (mtt180) cc_final: 0.7676 (mmt-90) REVERT: A 227 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.7675 (ttp80) REVERT: A 240 LEU cc_start: 0.9084 (tt) cc_final: 0.8737 (tt) REVERT: A 251 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8315 (mm-30) REVERT: A 291 ASP cc_start: 0.8421 (m-30) cc_final: 0.8164 (m-30) REVERT: A 308 LYS cc_start: 0.9012 (mttt) cc_final: 0.8684 (mttm) REVERT: A 355 ASN cc_start: 0.8502 (p0) cc_final: 0.8172 (p0) REVERT: A 369 TRP cc_start: 0.9101 (t60) cc_final: 0.8723 (t60) REVERT: A 499 HIS cc_start: 0.8513 (m-70) cc_final: 0.8081 (p-80) REVERT: A 526 ASP cc_start: 0.8980 (t70) cc_final: 0.8269 (t70) REVERT: A 533 GLN cc_start: 0.9257 (tm-30) cc_final: 0.8732 (tm-30) REVERT: B 9 GLN cc_start: 0.8847 (mp10) cc_final: 0.8374 (pt0) REVERT: B 12 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8491 (mm-30) REVERT: B 37 MET cc_start: 0.9506 (mmm) cc_final: 0.9270 (mmm) REVERT: B 46 GLU cc_start: 0.9150 (tp30) cc_final: 0.8915 (tp30) REVERT: B 52 MET cc_start: 0.9201 (mtm) cc_final: 0.8781 (mtm) REVERT: B 54 ASN cc_start: 0.9274 (m-40) cc_final: 0.8878 (m110) REVERT: B 56 VAL cc_start: 0.8982 (t) cc_final: 0.8750 (p) REVERT: B 64 ILE cc_start: 0.9490 (mm) cc_final: 0.9257 (mm) REVERT: B 72 MET cc_start: 0.9367 (ptm) cc_final: 0.8962 (tmm) REVERT: B 115 GLU cc_start: 0.8764 (mp0) cc_final: 0.8148 (mp0) REVERT: B 117 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8596 (mt) REVERT: B 120 GLU cc_start: 0.9100 (tp30) cc_final: 0.8884 (mm-30) REVERT: B 121 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8444 (mm-30) REVERT: B 125 MET cc_start: 0.9512 (ttt) cc_final: 0.9186 (ttt) REVERT: C 166 TRP cc_start: 0.8571 (t60) cc_final: 0.8093 (t60) REVERT: C 180 ARG cc_start: 0.8186 (mtt180) cc_final: 0.7606 (mtt-85) REVERT: C 227 ARG cc_start: 0.9242 (OUTLIER) cc_final: 0.7732 (ttp80) REVERT: C 240 LEU cc_start: 0.9083 (tt) cc_final: 0.8361 (tt) REVERT: C 251 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8363 (mm-30) REVERT: C 291 ASP cc_start: 0.8421 (m-30) cc_final: 0.8162 (m-30) REVERT: C 308 LYS cc_start: 0.9002 (mttt) cc_final: 0.8675 (mttm) REVERT: C 343 LEU cc_start: 0.9011 (mt) cc_final: 0.8652 (mp) REVERT: C 355 ASN cc_start: 0.8512 (p0) cc_final: 0.8187 (p0) REVERT: C 369 TRP cc_start: 0.9100 (t60) cc_final: 0.8714 (t60) REVERT: C 499 HIS cc_start: 0.8516 (m-70) cc_final: 0.8082 (p-80) REVERT: C 526 ASP cc_start: 0.8975 (t70) cc_final: 0.8268 (t70) REVERT: D 9 GLN cc_start: 0.8844 (mp10) cc_final: 0.8371 (pt0) REVERT: D 12 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8498 (mm-30) REVERT: D 37 MET cc_start: 0.9508 (mmm) cc_final: 0.9274 (mmm) REVERT: D 46 GLU cc_start: 0.9151 (tp30) cc_final: 0.8917 (tp30) REVERT: D 52 MET cc_start: 0.9200 (mtm) cc_final: 0.8779 (mtm) REVERT: D 54 ASN cc_start: 0.9275 (m-40) cc_final: 0.8877 (m110) REVERT: D 56 VAL cc_start: 0.8983 (t) cc_final: 0.8751 (p) REVERT: D 64 ILE cc_start: 0.9492 (mm) cc_final: 0.9258 (mm) REVERT: D 72 MET cc_start: 0.9367 (ptm) cc_final: 0.8961 (tmm) REVERT: D 115 GLU cc_start: 0.8763 (mp0) cc_final: 0.8146 (mp0) REVERT: D 117 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8581 (mt) REVERT: D 121 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8420 (mm-30) REVERT: D 125 MET cc_start: 0.9506 (ttt) cc_final: 0.9185 (ttt) REVERT: E 166 TRP cc_start: 0.8563 (t60) cc_final: 0.8123 (t60) REVERT: E 180 ARG cc_start: 0.8187 (mtt180) cc_final: 0.7683 (mmt-90) REVERT: E 227 ARG cc_start: 0.9248 (OUTLIER) cc_final: 0.7720 (ttp80) REVERT: E 240 LEU cc_start: 0.9083 (tt) cc_final: 0.8733 (tt) REVERT: E 251 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8309 (mm-30) REVERT: E 291 ASP cc_start: 0.8424 (m-30) cc_final: 0.8165 (m-30) REVERT: E 308 LYS cc_start: 0.9010 (mttt) cc_final: 0.8682 (mttm) REVERT: E 355 ASN cc_start: 0.8510 (p0) cc_final: 0.8182 (p0) REVERT: E 369 TRP cc_start: 0.9095 (t60) cc_final: 0.8720 (t60) REVERT: E 499 HIS cc_start: 0.8515 (m-70) cc_final: 0.8082 (p-80) REVERT: E 526 ASP cc_start: 0.8981 (t70) cc_final: 0.8273 (t70) REVERT: F 9 GLN cc_start: 0.8844 (mp10) cc_final: 0.8372 (pt0) REVERT: F 12 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8487 (mm-30) REVERT: F 37 MET cc_start: 0.9508 (mmm) cc_final: 0.9274 (mmm) REVERT: F 46 GLU cc_start: 0.9150 (tp30) cc_final: 0.8918 (tp30) REVERT: F 52 MET cc_start: 0.9199 (mtm) cc_final: 0.8780 (mtm) REVERT: F 54 ASN cc_start: 0.9274 (m-40) cc_final: 0.8879 (m110) REVERT: F 56 VAL cc_start: 0.8982 (t) cc_final: 0.8752 (p) REVERT: F 64 ILE cc_start: 0.9494 (mm) cc_final: 0.9257 (mm) REVERT: F 72 MET cc_start: 0.9377 (ptm) cc_final: 0.8961 (tmm) REVERT: F 115 GLU cc_start: 0.8765 (mp0) cc_final: 0.8149 (mp0) REVERT: F 117 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8580 (mt) REVERT: F 121 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8434 (mm-30) REVERT: F 125 MET cc_start: 0.9512 (ttt) cc_final: 0.9190 (ttt) REVERT: G 166 TRP cc_start: 0.8570 (t60) cc_final: 0.8093 (t60) REVERT: G 180 ARG cc_start: 0.8185 (mtt180) cc_final: 0.7604 (mtt-85) REVERT: G 227 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.7774 (ttp80) REVERT: G 240 LEU cc_start: 0.9083 (tt) cc_final: 0.8361 (tt) REVERT: G 251 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8372 (mm-30) REVERT: G 291 ASP cc_start: 0.8423 (m-30) cc_final: 0.8165 (m-30) REVERT: G 308 LYS cc_start: 0.9014 (mttt) cc_final: 0.8685 (mttm) REVERT: G 343 LEU cc_start: 0.9010 (mt) cc_final: 0.8650 (mp) REVERT: G 355 ASN cc_start: 0.8510 (p0) cc_final: 0.8183 (p0) REVERT: G 369 TRP cc_start: 0.9105 (t60) cc_final: 0.8726 (t60) REVERT: G 499 HIS cc_start: 0.8515 (m-70) cc_final: 0.8083 (p-80) REVERT: G 526 ASP cc_start: 0.8976 (t70) cc_final: 0.8268 (t70) REVERT: G 550 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8638 (ttp80) REVERT: H 9 GLN cc_start: 0.8844 (mp10) cc_final: 0.8371 (pt0) REVERT: H 12 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8479 (mm-30) REVERT: H 37 MET cc_start: 0.9510 (mmm) cc_final: 0.9276 (mmm) REVERT: H 46 GLU cc_start: 0.9150 (tp30) cc_final: 0.8917 (tp30) REVERT: H 52 MET cc_start: 0.9182 (mtm) cc_final: 0.8756 (mtm) REVERT: H 54 ASN cc_start: 0.9203 (m-40) cc_final: 0.8816 (m110) REVERT: H 56 VAL cc_start: 0.8845 (t) cc_final: 0.8484 (p) REVERT: H 72 MET cc_start: 0.9284 (ptm) cc_final: 0.8863 (tmm) REVERT: H 115 GLU cc_start: 0.8761 (mp0) cc_final: 0.8146 (mp0) REVERT: H 117 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8574 (mt) REVERT: H 121 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8432 (mm-30) REVERT: H 125 MET cc_start: 0.9510 (ttt) cc_final: 0.9188 (ttt) outliers start: 94 outliers final: 62 residues processed: 678 average time/residue: 0.1086 time to fit residues: 112.8928 Evaluate side-chains 713 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 638 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 121 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 152 VAL 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 254 THR Chi-restraints excluded: chain A residue 261 LEU 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 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 118 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 152 VAL 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 254 THR Chi-restraints excluded: chain C residue 261 LEU 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 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 118 THR Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 152 VAL 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 254 THR Chi-restraints excluded: chain E residue 261 LEU 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 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 118 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 152 VAL 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 254 THR Chi-restraints excluded: chain G residue 261 LEU 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 550 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 88 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 chunk 187 optimal weight: 0.0370 chunk 97 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 HIS B 112 ASN C 353 HIS D 112 ASN E 353 HIS F 112 ASN G 353 HIS H 112 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.091749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.075199 restraints weight = 38406.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.077953 restraints weight = 19462.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.079907 restraints weight = 12280.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.081276 restraints weight = 8720.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.082229 restraints weight = 6767.739| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4217 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= 0.137 Angle : 0.569 9.056 20644 Z= 0.290 Chirality : 0.038 0.177 2368 Planarity : 0.004 0.036 2576 Dihedral : 3.627 17.533 2104 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 5.46 % Allowed : 26.45 % Favored : 68.09 % 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: 3.14 (0.13), residues: 1500 sheet: None (None), residues: 0 loop : -0.88 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 91 TYR 0.018 0.002 TYR A 268 PHE 0.017 0.002 PHE C 260 TRP 0.007 0.001 TRP G 295 HIS 0.004 0.001 HIS F 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (15228) covalent geometry : angle 0.56916 / 0.29 (20644) hydrogen bonds : bond 0.03594 / 2.46 ( 1112) hydrogen bonds : angle 3.89482 / 2.91 ( 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 715 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 636 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.8592 (t60) cc_final: 0.8149 (t60) REVERT: A 180 ARG cc_start: 0.8226 (mtt180) cc_final: 0.7699 (mmt-90) REVERT: A 227 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.7766 (ttp80) REVERT: A 251 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8431 (mm-30) REVERT: A 291 ASP cc_start: 0.8433 (m-30) cc_final: 0.8189 (m-30) REVERT: A 308 LYS cc_start: 0.9025 (mttt) cc_final: 0.8675 (mttm) REVERT: A 355 ASN cc_start: 0.8553 (p0) cc_final: 0.8272 (p0) REVERT: A 369 TRP cc_start: 0.9154 (t60) cc_final: 0.8738 (t60) REVERT: A 499 HIS cc_start: 0.8488 (m-70) cc_final: 0.8027 (p-80) REVERT: A 526 ASP cc_start: 0.8978 (t70) cc_final: 0.8270 (t70) REVERT: A 533 GLN cc_start: 0.9290 (tm-30) cc_final: 0.9002 (tm-30) REVERT: A 534 TYR cc_start: 0.8921 (t80) cc_final: 0.7511 (t80) REVERT: B 12 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8480 (mm-30) REVERT: B 37 MET cc_start: 0.9494 (mmm) cc_final: 0.9223 (mmm) REVERT: B 46 GLU cc_start: 0.9147 (tp30) cc_final: 0.8903 (tp30) REVERT: B 52 MET cc_start: 0.9167 (mtm) cc_final: 0.8741 (mtm) REVERT: B 54 ASN cc_start: 0.9207 (m-40) cc_final: 0.8774 (m110) REVERT: B 64 ILE cc_start: 0.9482 (mm) cc_final: 0.9258 (mm) REVERT: B 72 MET cc_start: 0.9330 (ptm) cc_final: 0.8995 (tmm) REVERT: B 115 GLU cc_start: 0.8760 (mp0) cc_final: 0.8106 (mp0) REVERT: B 117 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8595 (mt) REVERT: B 120 GLU cc_start: 0.9090 (tp30) cc_final: 0.8881 (mm-30) REVERT: B 121 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8302 (mm-30) REVERT: B 125 MET cc_start: 0.9500 (ttt) cc_final: 0.9171 (ttt) REVERT: C 104 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9051 (tp) REVERT: C 166 TRP cc_start: 0.8600 (t60) cc_final: 0.8136 (t60) REVERT: C 180 ARG cc_start: 0.8228 (mtt180) cc_final: 0.7622 (mtt-85) REVERT: C 227 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.7719 (ttp80) REVERT: C 291 ASP cc_start: 0.8431 (m-30) cc_final: 0.8187 (m-30) REVERT: C 308 LYS cc_start: 0.8963 (mttt) cc_final: 0.8620 (mttm) REVERT: C 343 LEU cc_start: 0.9020 (mt) cc_final: 0.8636 (mp) REVERT: C 355 ASN cc_start: 0.8554 (p0) cc_final: 0.8271 (p0) REVERT: C 369 TRP cc_start: 0.9152 (t60) cc_final: 0.8729 (t60) REVERT: C 499 HIS cc_start: 0.8486 (m-70) cc_final: 0.8024 (p-80) REVERT: C 526 ASP cc_start: 0.8969 (t70) cc_final: 0.8265 (t70) REVERT: C 534 TYR cc_start: 0.8980 (t80) cc_final: 0.8289 (t80) REVERT: D 12 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8498 (mm-30) REVERT: D 37 MET cc_start: 0.9495 (mmm) cc_final: 0.9229 (mmm) REVERT: D 46 GLU cc_start: 0.9147 (tp30) cc_final: 0.8904 (tp30) REVERT: D 52 MET cc_start: 0.9169 (mtm) cc_final: 0.8742 (mtm) REVERT: D 54 ASN cc_start: 0.9209 (m-40) cc_final: 0.8776 (m110) REVERT: D 64 ILE cc_start: 0.9483 (mm) cc_final: 0.9261 (mm) REVERT: D 72 MET cc_start: 0.9335 (ptm) cc_final: 0.8994 (tmm) REVERT: D 115 GLU cc_start: 0.8757 (mp0) cc_final: 0.8103 (mp0) REVERT: D 117 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8632 (mt) REVERT: D 121 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8286 (mm-30) REVERT: D 125 MET cc_start: 0.9494 (ttt) cc_final: 0.9168 (ttt) REVERT: E 166 TRP cc_start: 0.8601 (t60) cc_final: 0.8162 (t60) REVERT: E 180 ARG cc_start: 0.8232 (mtt180) cc_final: 0.7707 (mmt-90) REVERT: E 227 ARG cc_start: 0.9216 (OUTLIER) cc_final: 0.7761 (ttp80) REVERT: E 251 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8431 (mm-30) REVERT: E 291 ASP cc_start: 0.8437 (m-30) cc_final: 0.8191 (m-30) REVERT: E 308 LYS cc_start: 0.9026 (mttt) cc_final: 0.8676 (mttm) REVERT: E 355 ASN cc_start: 0.8553 (p0) cc_final: 0.8269 (p0) REVERT: E 369 TRP cc_start: 0.9148 (t60) cc_final: 0.8731 (t60) REVERT: E 499 HIS cc_start: 0.8485 (m-70) cc_final: 0.8023 (p-80) REVERT: E 526 ASP cc_start: 0.8979 (t70) cc_final: 0.8276 (t70) REVERT: E 534 TYR cc_start: 0.8956 (t80) cc_final: 0.8316 (t80) REVERT: F 12 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8483 (mm-30) REVERT: F 37 MET cc_start: 0.9496 (mmm) cc_final: 0.9227 (mmm) REVERT: F 46 GLU cc_start: 0.9147 (tp30) cc_final: 0.8905 (tp30) REVERT: F 52 MET cc_start: 0.9170 (mtm) cc_final: 0.8743 (mtm) REVERT: F 54 ASN cc_start: 0.9210 (m-40) cc_final: 0.8774 (m110) REVERT: F 64 ILE cc_start: 0.9488 (mm) cc_final: 0.9261 (mm) REVERT: F 72 MET cc_start: 0.9337 (ptm) cc_final: 0.9001 (tmm) REVERT: F 115 GLU cc_start: 0.8760 (mp0) cc_final: 0.8106 (mp0) REVERT: F 117 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8634 (mt) REVERT: F 121 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8299 (mm-30) REVERT: F 125 MET cc_start: 0.9499 (ttt) cc_final: 0.9170 (ttt) REVERT: G 104 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9046 (tp) REVERT: G 166 TRP cc_start: 0.8596 (t60) cc_final: 0.8133 (t60) REVERT: G 180 ARG cc_start: 0.8226 (mtt180) cc_final: 0.7618 (mtt-85) REVERT: G 227 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.7721 (ttp80) REVERT: G 291 ASP cc_start: 0.8433 (m-30) cc_final: 0.8187 (m-30) REVERT: G 308 LYS cc_start: 0.8970 (mttt) cc_final: 0.8625 (mttm) REVERT: G 343 LEU cc_start: 0.9016 (mt) cc_final: 0.8634 (mp) REVERT: G 355 ASN cc_start: 0.8554 (p0) cc_final: 0.8273 (p0) REVERT: G 369 TRP cc_start: 0.9158 (t60) cc_final: 0.8739 (t60) REVERT: G 499 HIS cc_start: 0.8485 (m-70) cc_final: 0.8027 (p-80) REVERT: G 526 ASP cc_start: 0.8969 (t70) cc_final: 0.8265 (t70) REVERT: G 534 TYR cc_start: 0.9003 (t80) cc_final: 0.7461 (t80) REVERT: G 550 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8664 (ttp80) REVERT: H 12 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8441 (mm-30) REVERT: H 37 MET cc_start: 0.9494 (mmm) cc_final: 0.9229 (mmm) REVERT: H 46 GLU cc_start: 0.9151 (tp30) cc_final: 0.8908 (tp30) REVERT: H 52 MET cc_start: 0.9146 (mtm) cc_final: 0.8694 (mtm) REVERT: H 54 ASN cc_start: 0.9252 (m-40) cc_final: 0.8834 (m110) REVERT: H 56 VAL cc_start: 0.8868 (t) cc_final: 0.8569 (p) REVERT: H 72 MET cc_start: 0.9270 (ptm) cc_final: 0.8941 (tmm) REVERT: H 115 GLU cc_start: 0.8754 (mp0) cc_final: 0.8101 (mp0) REVERT: H 117 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8633 (mt) REVERT: H 121 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8293 (mm-30) REVERT: H 125 MET cc_start: 0.9497 (ttt) cc_final: 0.9170 (ttt) outliers start: 79 outliers final: 51 residues processed: 658 average time/residue: 0.1089 time to fit residues: 110.1442 Evaluate side-chains 686 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 622 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 152 VAL 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 254 THR Chi-restraints excluded: chain A residue 261 LEU 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 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 118 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 513 VAL 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 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 118 THR Chi-restraints excluded: chain E residue 152 VAL 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 254 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain F residue 19 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 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 118 THR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 550 ARG 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 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: 0.7980 chunk 103 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 85 optimal weight: 0.0870 chunk 92 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3302 r_free = 0.3302 target = 0.092370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.075913 restraints weight = 38355.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.078669 restraints weight = 19303.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.080595 restraints weight = 12145.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.081969 restraints weight = 8675.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.082947 restraints weight = 6731.877| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4354 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= 0.129 Angle : 0.596 11.317 20644 Z= 0.297 Chirality : 0.039 0.225 2368 Planarity : 0.005 0.066 2576 Dihedral : 3.558 18.311 2104 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 5.04 % Allowed : 27.69 % Favored : 67.27 % 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: 3.50 (0.20), residues: 1904 helix: 3.13 (0.13), residues: 1492 sheet: None (None), residues: 0 loop : -0.98 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 127 TYR 0.018 0.001 TYR E 268 PHE 0.017 0.001 PHE G 260 TRP 0.007 0.001 TRP G 295 HIS 0.004 0.001 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (15228) covalent geometry : angle 0.59568 / 0.30 (20644) hydrogen bonds : bond 0.03482 / 2.37 ( 1112) hydrogen bonds : angle 3.83743 / 2.88 ( 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 740 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 667 time to evaluate : 0.587 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: 0.8497 (t60) cc_final: 0.8062 (t60) REVERT: A 180 ARG cc_start: 0.8228 (mtt180) cc_final: 0.7666 (mmt-90) REVERT: A 227 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.7640 (ttp80) REVERT: A 291 ASP cc_start: 0.8417 (m-30) cc_final: 0.8186 (m-30) REVERT: A 308 LYS cc_start: 0.8923 (mttt) cc_final: 0.8588 (mttm) REVERT: A 355 ASN cc_start: 0.8513 (p0) cc_final: 0.8258 (p0) REVERT: A 369 TRP cc_start: 0.9135 (t60) cc_final: 0.8731 (t60) REVERT: A 499 HIS cc_start: 0.8488 (m-70) cc_final: 0.8061 (p-80) REVERT: A 526 ASP cc_start: 0.8986 (t70) cc_final: 0.8315 (t70) REVERT: A 533 GLN cc_start: 0.9053 (tm-30) cc_final: 0.8626 (tm-30) REVERT: A 534 TYR cc_start: 0.8817 (t80) cc_final: 0.6480 (t80) REVERT: B 9 GLN cc_start: 0.8866 (mp10) cc_final: 0.8591 (pm20) REVERT: B 12 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8439 (mm-30) REVERT: B 37 MET cc_start: 0.9494 (mmm) cc_final: 0.9264 (mmm) REVERT: B 52 MET cc_start: 0.9177 (mtm) cc_final: 0.8750 (mtm) REVERT: B 54 ASN cc_start: 0.9152 (m-40) cc_final: 0.8693 (m110) REVERT: B 72 MET cc_start: 0.9396 (ptm) cc_final: 0.9036 (tmm) REVERT: B 115 GLU cc_start: 0.8736 (mp0) cc_final: 0.7962 (mp0) REVERT: B 117 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8530 (mt) REVERT: B 121 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8294 (mm-30) REVERT: B 124 GLU cc_start: 0.9062 (tp30) cc_final: 0.8430 (tp30) REVERT: B 125 MET cc_start: 0.9524 (ttt) cc_final: 0.9222 (ttt) REVERT: B 127 ARG cc_start: 0.9234 (ttm110) cc_final: 0.8820 (ttp-110) REVERT: C 104 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8913 (tp) REVERT: C 133 SER cc_start: 0.8755 (p) cc_final: 0.8546 (p) REVERT: C 166 TRP cc_start: 0.8563 (t60) cc_final: 0.8097 (t60) REVERT: C 180 ARG cc_start: 0.8153 (mtt180) cc_final: 0.7507 (mmt-90) REVERT: C 193 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9189 (mp) REVERT: C 227 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.7710 (ttp80) REVERT: C 229 LEU cc_start: 0.9775 (mt) cc_final: 0.9535 (mm) REVERT: C 291 ASP cc_start: 0.8414 (m-30) cc_final: 0.8184 (m-30) REVERT: C 308 LYS cc_start: 0.8916 (mttt) cc_final: 0.8581 (mttm) REVERT: C 343 LEU cc_start: 0.8974 (mt) cc_final: 0.8586 (mp) REVERT: C 355 ASN cc_start: 0.8518 (p0) cc_final: 0.8226 (p0) REVERT: C 369 TRP cc_start: 0.9130 (t60) cc_final: 0.8720 (t60) REVERT: C 499 HIS cc_start: 0.8486 (m-70) cc_final: 0.8059 (p-80) REVERT: C 526 ASP cc_start: 0.8982 (t70) cc_final: 0.8310 (t70) REVERT: C 534 TYR cc_start: 0.8846 (t80) cc_final: 0.6382 (t80) REVERT: D 9 GLN cc_start: 0.8862 (mp10) cc_final: 0.8588 (pm20) REVERT: D 12 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8459 (mm-30) REVERT: D 37 MET cc_start: 0.9490 (mmm) cc_final: 0.9263 (mmm) REVERT: D 52 MET cc_start: 0.9182 (mtm) cc_final: 0.8752 (mtm) REVERT: D 54 ASN cc_start: 0.9153 (m-40) cc_final: 0.8695 (m110) REVERT: D 72 MET cc_start: 0.9399 (ptm) cc_final: 0.9033 (tmm) REVERT: D 115 GLU cc_start: 0.8737 (mp0) cc_final: 0.7963 (mp0) REVERT: D 117 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8645 (mt) REVERT: D 121 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8284 (mm-30) REVERT: D 124 GLU cc_start: 0.9057 (tp30) cc_final: 0.8427 (tp30) REVERT: D 125 MET cc_start: 0.9522 (ttt) cc_final: 0.9222 (ttt) REVERT: D 127 ARG cc_start: 0.9233 (ttm110) cc_final: 0.8822 (ttp-110) REVERT: E 166 TRP cc_start: 0.8487 (t60) cc_final: 0.8002 (t60) REVERT: E 180 ARG cc_start: 0.8233 (mtt180) cc_final: 0.7673 (mmt-90) REVERT: E 227 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.7633 (ttp80) REVERT: E 291 ASP cc_start: 0.8419 (m-30) cc_final: 0.8187 (m-30) REVERT: E 308 LYS cc_start: 0.8927 (mttt) cc_final: 0.8590 (mttm) REVERT: E 355 ASN cc_start: 0.8517 (p0) cc_final: 0.8257 (p0) REVERT: E 369 TRP cc_start: 0.9130 (t60) cc_final: 0.8730 (t60) REVERT: E 499 HIS cc_start: 0.8485 (m-70) cc_final: 0.8058 (p-80) REVERT: E 526 ASP cc_start: 0.8991 (t70) cc_final: 0.8324 (t70) REVERT: E 534 TYR cc_start: 0.8866 (t80) cc_final: 0.6446 (t80) REVERT: F 9 GLN cc_start: 0.8862 (mp10) cc_final: 0.8588 (pm20) REVERT: F 12 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8448 (mm-30) REVERT: F 37 MET cc_start: 0.9495 (mmm) cc_final: 0.9265 (mmm) REVERT: F 52 MET cc_start: 0.9185 (mtm) cc_final: 0.8755 (mtm) REVERT: F 54 ASN cc_start: 0.9152 (m-40) cc_final: 0.8693 (m110) REVERT: F 72 MET cc_start: 0.9392 (ptm) cc_final: 0.9043 (tmm) REVERT: F 115 GLU cc_start: 0.8742 (mp0) cc_final: 0.7969 (mp0) REVERT: F 117 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8603 (mt) REVERT: F 121 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8302 (mm-30) REVERT: F 124 GLU cc_start: 0.9060 (tp30) cc_final: 0.8435 (tp30) REVERT: F 125 MET cc_start: 0.9531 (ttt) cc_final: 0.9229 (ttt) REVERT: F 127 ARG cc_start: 0.9234 (ttm110) cc_final: 0.8823 (ttp-110) REVERT: G 133 SER cc_start: 0.8755 (p) cc_final: 0.8547 (p) REVERT: G 166 TRP cc_start: 0.8565 (t60) cc_final: 0.8036 (t60) REVERT: G 180 ARG cc_start: 0.8154 (mtt180) cc_final: 0.7504 (mmt-90) REVERT: G 193 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9190 (mp) REVERT: G 227 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.7706 (ttp80) REVERT: G 291 ASP cc_start: 0.8417 (m-30) cc_final: 0.8185 (m-30) REVERT: G 308 LYS cc_start: 0.8922 (mttt) cc_final: 0.8585 (mttm) REVERT: G 343 LEU cc_start: 0.8968 (mt) cc_final: 0.8582 (mp) REVERT: G 355 ASN cc_start: 0.8519 (p0) cc_final: 0.8225 (p0) REVERT: G 369 TRP cc_start: 0.9139 (t60) cc_final: 0.8734 (t60) REVERT: G 499 HIS cc_start: 0.8484 (m-70) cc_final: 0.8063 (p-80) REVERT: G 526 ASP cc_start: 0.8987 (t70) cc_final: 0.8314 (t70) REVERT: G 534 TYR cc_start: 0.8851 (t80) cc_final: 0.6379 (t80) REVERT: G 550 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8690 (ttp80) REVERT: H 9 GLN cc_start: 0.8871 (mp10) cc_final: 0.8596 (pm20) REVERT: H 12 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8443 (mm-30) REVERT: H 37 MET cc_start: 0.9494 (mmm) cc_final: 0.9265 (mmm) REVERT: H 52 MET cc_start: 0.9149 (mtm) cc_final: 0.8747 (mtm) REVERT: H 54 ASN cc_start: 0.9212 (m-40) cc_final: 0.8776 (m110) REVERT: H 56 VAL cc_start: 0.8874 (t) cc_final: 0.8577 (p) REVERT: H 72 MET cc_start: 0.9324 (ptm) cc_final: 0.8965 (tmm) REVERT: H 75 ARG cc_start: 0.8494 (ptt-90) cc_final: 0.8114 (tmm-80) REVERT: H 115 GLU cc_start: 0.8737 (mp0) cc_final: 0.7963 (mp0) REVERT: H 117 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8604 (mt) REVERT: H 121 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8290 (mm-30) REVERT: H 124 GLU cc_start: 0.9060 (tp30) cc_final: 0.8430 (tp30) REVERT: H 125 MET cc_start: 0.9527 (ttt) cc_final: 0.9226 (ttt) REVERT: H 127 ARG cc_start: 0.9235 (ttm110) cc_final: 0.8824 (ttp-110) outliers start: 73 outliers final: 47 residues processed: 688 average time/residue: 0.1070 time to fit residues: 113.1260 Evaluate side-chains 694 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 635 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 190 VAL Chi-restraints excluded: chain A residue 194 ILE 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 513 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 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 118 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 193 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 255 THR Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain D residue 19 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 D residue 146 MET Chi-restraints excluded: chain E residue 110 TRP Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 190 VAL 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 513 VAL Chi-restraints excluded: chain F residue 19 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 F residue 146 MET Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 193 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 255 THR Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 550 ARG Chi-restraints excluded: chain H residue 19 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 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: 4.9990 chunk 61 optimal weight: 0.2980 chunk 139 optimal weight: 0.2980 chunk 130 optimal weight: 2.9990 chunk 185 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 119 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.091945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.075413 restraints weight = 38894.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.078221 restraints weight = 19191.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.080163 restraints weight = 11940.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.081531 restraints weight = 8464.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.082446 restraints weight = 6546.178| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15228 Z= 0.145 Angle : 0.620 9.924 20644 Z= 0.310 Chirality : 0.039 0.218 2368 Planarity : 0.004 0.043 2576 Dihedral : 3.527 17.951 2104 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 6.08 % Allowed : 27.76 % Favored : 66.16 % 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: 3.00 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.12 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 127 TYR 0.019 0.001 TYR A 268 PHE 0.021 0.002 PHE F 17 TRP 0.007 0.001 TRP A 295 HIS 0.003 0.001 HIS G 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (15228) covalent geometry : angle 0.62033 / 0.31 (20644) hydrogen bonds : bond 0.03559 / 2.42 ( 1112) hydrogen bonds : angle 3.89196 / 2.92 ( 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 739 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 651 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.8500 (t60) cc_final: 0.8013 (t60) REVERT: A 180 ARG cc_start: 0.8271 (mtt180) cc_final: 0.7678 (mmt-90) REVERT: A 227 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.7568 (ttp80) REVERT: A 291 ASP cc_start: 0.8425 (m-30) cc_final: 0.8202 (m-30) REVERT: A 308 LYS cc_start: 0.8934 (mttt) cc_final: 0.8594 (mttm) REVERT: A 355 ASN cc_start: 0.8512 (p0) cc_final: 0.8266 (p0) REVERT: A 369 TRP cc_start: 0.9136 (t60) cc_final: 0.8730 (t60) REVERT: A 499 HIS cc_start: 0.8511 (m-70) cc_final: 0.8085 (p-80) REVERT: A 526 ASP cc_start: 0.9004 (t70) cc_final: 0.8333 (t70) REVERT: A 533 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8566 (tm-30) REVERT: B 9 GLN cc_start: 0.8833 (mp10) cc_final: 0.8558 (pm20) REVERT: B 12 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8426 (mm-30) REVERT: B 37 MET cc_start: 0.9437 (mmm) cc_final: 0.9209 (mmm) REVERT: B 52 MET cc_start: 0.9179 (mtm) cc_final: 0.8742 (mtm) REVERT: B 54 ASN cc_start: 0.9188 (m-40) cc_final: 0.8747 (m110) REVERT: B 72 MET cc_start: 0.9424 (ptm) cc_final: 0.9096 (tmm) REVERT: B 112 ASN cc_start: 0.8690 (m-40) cc_final: 0.8284 (m110) REVERT: B 115 GLU cc_start: 0.8843 (mp0) cc_final: 0.8354 (mp0) REVERT: B 121 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8367 (mm-30) REVERT: B 125 MET cc_start: 0.9542 (ttt) cc_final: 0.9218 (ttt) REVERT: C 104 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8949 (tp) REVERT: C 166 TRP cc_start: 0.8568 (t60) cc_final: 0.8045 (t60) REVERT: C 180 ARG cc_start: 0.8266 (mtt180) cc_final: 0.7674 (mmt-90) REVERT: C 193 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9217 (mp) REVERT: C 229 LEU cc_start: 0.9784 (mt) cc_final: 0.9564 (mm) REVERT: C 291 ASP cc_start: 0.8424 (m-30) cc_final: 0.8197 (m-30) REVERT: C 308 LYS cc_start: 0.8930 (mttt) cc_final: 0.8587 (mttm) REVERT: C 355 ASN cc_start: 0.8434 (p0) cc_final: 0.8213 (p0) REVERT: C 369 TRP cc_start: 0.9127 (t60) cc_final: 0.8718 (t60) REVERT: C 499 HIS cc_start: 0.8513 (m-70) cc_final: 0.8082 (p-80) REVERT: C 526 ASP cc_start: 0.9002 (t70) cc_final: 0.8324 (t70) REVERT: D 9 GLN cc_start: 0.8830 (mp10) cc_final: 0.8554 (pm20) REVERT: D 12 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8439 (mm-30) REVERT: D 37 MET cc_start: 0.9437 (mmm) cc_final: 0.9211 (mmm) REVERT: D 52 MET cc_start: 0.9180 (mtm) cc_final: 0.8746 (mtm) REVERT: D 54 ASN cc_start: 0.9190 (m-40) cc_final: 0.8749 (m110) REVERT: D 72 MET cc_start: 0.9426 (ptm) cc_final: 0.9092 (tmm) REVERT: D 115 GLU cc_start: 0.8843 (mp0) cc_final: 0.8358 (mp0) REVERT: D 121 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8344 (mm-30) REVERT: D 125 MET cc_start: 0.9538 (ttt) cc_final: 0.9220 (ttt) REVERT: E 166 TRP cc_start: 0.8509 (t60) cc_final: 0.8028 (t60) REVERT: E 180 ARG cc_start: 0.8275 (mtt180) cc_final: 0.7681 (mmt-90) REVERT: E 227 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.7566 (ttp80) REVERT: E 291 ASP cc_start: 0.8428 (m-30) cc_final: 0.8203 (m-30) REVERT: E 308 LYS cc_start: 0.8939 (mttt) cc_final: 0.8596 (mttm) REVERT: E 355 ASN cc_start: 0.8524 (p0) cc_final: 0.8270 (p0) REVERT: E 369 TRP cc_start: 0.9126 (t60) cc_final: 0.8726 (t60) REVERT: E 499 HIS cc_start: 0.8510 (m-70) cc_final: 0.8081 (p-80) REVERT: E 526 ASP cc_start: 0.9011 (t70) cc_final: 0.8342 (t70) REVERT: F 9 GLN cc_start: 0.8829 (mp10) cc_final: 0.8555 (pm20) REVERT: F 12 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8435 (mm-30) REVERT: F 37 MET cc_start: 0.9440 (mmm) cc_final: 0.9214 (mmm) REVERT: F 52 MET cc_start: 0.9183 (mtm) cc_final: 0.8744 (mtm) REVERT: F 54 ASN cc_start: 0.9193 (m-40) cc_final: 0.8731 (m110) REVERT: F 72 MET cc_start: 0.9416 (ptm) cc_final: 0.9102 (tmm) REVERT: F 112 ASN cc_start: 0.8687 (m-40) cc_final: 0.8283 (m110) REVERT: F 115 GLU cc_start: 0.8845 (mp0) cc_final: 0.8359 (mp0) REVERT: F 121 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8359 (mm-30) REVERT: F 125 MET cc_start: 0.9546 (ttt) cc_final: 0.9224 (ttt) REVERT: G 104 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9061 (tp) REVERT: G 121 LEU cc_start: 0.9443 (tp) cc_final: 0.9189 (mm) REVERT: G 166 TRP cc_start: 0.8571 (t60) cc_final: 0.8052 (t60) REVERT: G 180 ARG cc_start: 0.8266 (mtt180) cc_final: 0.7672 (mmt-90) REVERT: G 227 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.7667 (ttp80) REVERT: G 291 ASP cc_start: 0.8426 (m-30) cc_final: 0.8199 (m-30) REVERT: G 308 LYS cc_start: 0.8934 (mttt) cc_final: 0.8591 (mttm) REVERT: G 355 ASN cc_start: 0.8437 (p0) cc_final: 0.8215 (p0) REVERT: G 369 TRP cc_start: 0.9135 (t60) cc_final: 0.8733 (t60) REVERT: G 499 HIS cc_start: 0.8505 (m-70) cc_final: 0.8085 (p-80) REVERT: G 526 ASP cc_start: 0.9008 (t70) cc_final: 0.8330 (t70) REVERT: G 534 TYR cc_start: 0.8813 (t80) cc_final: 0.8328 (t80) REVERT: G 550 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8708 (ttp80) REVERT: H 9 GLN cc_start: 0.8847 (mp10) cc_final: 0.8565 (pm20) REVERT: H 12 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8500 (mm-30) REVERT: H 37 MET cc_start: 0.9438 (mmm) cc_final: 0.9215 (mmm) REVERT: H 52 MET cc_start: 0.9141 (mtm) cc_final: 0.8723 (mtm) REVERT: H 54 ASN cc_start: 0.9201 (m-40) cc_final: 0.8764 (m110) REVERT: H 56 VAL cc_start: 0.8888 (t) cc_final: 0.8606 (p) REVERT: H 72 MET cc_start: 0.9383 (ptm) cc_final: 0.8998 (tmm) REVERT: H 112 ASN cc_start: 0.8687 (m-40) cc_final: 0.8280 (m110) REVERT: H 115 GLU cc_start: 0.8843 (mp0) cc_final: 0.8360 (mp0) REVERT: H 121 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8347 (mm-30) REVERT: H 125 MET cc_start: 0.9544 (ttt) cc_final: 0.9223 (ttt) outliers start: 88 outliers final: 57 residues processed: 680 average time/residue: 0.1103 time to fit residues: 115.3380 Evaluate side-chains 694 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 630 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 190 VAL Chi-restraints excluded: chain A residue 194 ILE 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 513 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 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 118 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 513 VAL 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 190 VAL 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 513 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 167 SER Chi-restraints excluded: chain G residue 190 VAL 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 255 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 532 GLU Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 550 ARG Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 146 MET 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: 3.9990 chunk 101 optimal weight: 3.9990 chunk 159 optimal weight: 0.0870 chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 overall best weight: 1.2360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.092045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.075064 restraints weight = 39308.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.077822 restraints weight = 19930.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.079763 restraints weight = 12606.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.081116 restraints weight = 9047.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.082105 restraints weight = 7068.259| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15228 Z= 0.159 Angle : 0.609 10.875 20644 Z= 0.309 Chirality : 0.040 0.228 2368 Planarity : 0.004 0.040 2576 Dihedral : 3.516 18.645 2104 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 5.32 % Allowed : 28.94 % Favored : 65.75 % 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: 3.38 (0.20), residues: 1904 helix: 3.00 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.09 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 127 TYR 0.020 0.001 TYR E 268 PHE 0.020 0.002 PHE G 260 TRP 0.008 0.001 TRP C 369 HIS 0.002 0.001 HIS F 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (15228) covalent geometry : angle 0.60874 / 0.31 (20644) hydrogen bonds : bond 0.03464 / 2.36 ( 1112) hydrogen bonds : angle 3.96202 / 2.97 ( 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 709 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 632 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.8459 (t60) cc_final: 0.7965 (t60) REVERT: A 180 ARG cc_start: 0.8232 (mtt180) cc_final: 0.7563 (mtt-85) REVERT: A 227 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.7459 (ttp80) REVERT: A 291 ASP cc_start: 0.8434 (m-30) cc_final: 0.8215 (m-30) REVERT: A 308 LYS cc_start: 0.8948 (mttt) cc_final: 0.8605 (mttm) REVERT: A 355 ASN cc_start: 0.8513 (p0) cc_final: 0.8301 (p0) REVERT: A 369 TRP cc_start: 0.9137 (t60) cc_final: 0.8690 (t60) REVERT: A 499 HIS cc_start: 0.8567 (m-70) cc_final: 0.8094 (p-80) REVERT: A 526 ASP cc_start: 0.9030 (t70) cc_final: 0.8329 (t70) REVERT: A 533 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8534 (tm-30) REVERT: B 9 GLN cc_start: 0.8833 (mp10) cc_final: 0.8587 (pm20) REVERT: B 12 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8513 (mm-30) REVERT: B 37 MET cc_start: 0.9426 (mmm) cc_final: 0.9213 (tpp) REVERT: B 52 MET cc_start: 0.9202 (mtm) cc_final: 0.8727 (mtm) REVERT: B 54 ASN cc_start: 0.9194 (m-40) cc_final: 0.8751 (m110) REVERT: B 72 MET cc_start: 0.9438 (ptm) cc_final: 0.9067 (tmm) REVERT: B 112 ASN cc_start: 0.8674 (m-40) cc_final: 0.8253 (m110) REVERT: B 115 GLU cc_start: 0.8818 (mp0) cc_final: 0.7994 (mp0) REVERT: B 117 LEU cc_start: 0.8775 (mt) cc_final: 0.8314 (mt) REVERT: B 119 ASP cc_start: 0.9048 (p0) cc_final: 0.8818 (p0) REVERT: B 121 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8563 (mm-30) REVERT: B 125 MET cc_start: 0.9530 (ttt) cc_final: 0.9200 (ttt) REVERT: C 104 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8967 (tp) REVERT: C 166 TRP cc_start: 0.8572 (t60) cc_final: 0.8044 (t60) REVERT: C 180 ARG cc_start: 0.8232 (mtt180) cc_final: 0.7562 (mtt-85) REVERT: C 229 LEU cc_start: 0.9786 (mt) cc_final: 0.9553 (mm) REVERT: C 291 ASP cc_start: 0.8441 (m-30) cc_final: 0.8216 (m-30) REVERT: C 308 LYS cc_start: 0.8951 (mttt) cc_final: 0.8603 (mttm) REVERT: C 355 ASN cc_start: 0.8490 (p0) cc_final: 0.8272 (p0) REVERT: C 369 TRP cc_start: 0.9132 (t60) cc_final: 0.8681 (t60) REVERT: C 499 HIS cc_start: 0.8565 (m-70) cc_final: 0.8093 (p-80) REVERT: C 526 ASP cc_start: 0.9031 (t70) cc_final: 0.8325 (t70) REVERT: C 534 TYR cc_start: 0.8805 (t80) cc_final: 0.8393 (t80) REVERT: C 550 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8921 (mtp-110) REVERT: D 9 GLN cc_start: 0.8831 (mp10) cc_final: 0.8585 (pm20) REVERT: D 12 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8521 (mm-30) REVERT: D 37 MET cc_start: 0.9425 (mmm) cc_final: 0.9211 (tpp) REVERT: D 52 MET cc_start: 0.9209 (mtm) cc_final: 0.8730 (mtm) REVERT: D 54 ASN cc_start: 0.9192 (m-40) cc_final: 0.8750 (m110) REVERT: D 72 MET cc_start: 0.9438 (ptm) cc_final: 0.9063 (tmm) REVERT: D 115 GLU cc_start: 0.8823 (mp0) cc_final: 0.7998 (mp0) REVERT: D 117 LEU cc_start: 0.8770 (mt) cc_final: 0.8307 (mt) REVERT: D 120 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8773 (mm-30) REVERT: D 121 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8570 (mm-30) REVERT: D 125 MET cc_start: 0.9528 (ttt) cc_final: 0.9196 (ttt) REVERT: E 166 TRP cc_start: 0.8531 (t60) cc_final: 0.8037 (t60) REVERT: E 180 ARG cc_start: 0.8235 (mtt180) cc_final: 0.7566 (mtt-85) REVERT: E 227 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.7458 (ttp80) REVERT: E 291 ASP cc_start: 0.8436 (m-30) cc_final: 0.8217 (m-30) REVERT: E 308 LYS cc_start: 0.8953 (mttt) cc_final: 0.8615 (mttm) REVERT: E 355 ASN cc_start: 0.8531 (p0) cc_final: 0.8315 (p0) REVERT: E 369 TRP cc_start: 0.9131 (t60) cc_final: 0.8691 (t60) REVERT: E 499 HIS cc_start: 0.8564 (m-70) cc_final: 0.8091 (p-80) REVERT: E 526 ASP cc_start: 0.9039 (t70) cc_final: 0.8337 (t70) REVERT: F 9 GLN cc_start: 0.8830 (mp10) cc_final: 0.8584 (pm20) REVERT: F 12 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8524 (mm-30) REVERT: F 37 MET cc_start: 0.9430 (mmm) cc_final: 0.9187 (mmm) REVERT: F 52 MET cc_start: 0.9203 (mtm) cc_final: 0.8735 (mtm) REVERT: F 54 ASN cc_start: 0.9191 (m-40) cc_final: 0.8762 (m110) REVERT: F 72 MET cc_start: 0.9425 (ptm) cc_final: 0.9082 (tmm) REVERT: F 112 ASN cc_start: 0.8682 (m-40) cc_final: 0.8260 (m110) REVERT: F 115 GLU cc_start: 0.8819 (mp0) cc_final: 0.7989 (mp0) REVERT: F 117 LEU cc_start: 0.8771 (mt) cc_final: 0.8312 (mt) REVERT: F 120 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8780 (mm-30) REVERT: F 121 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8581 (mm-30) REVERT: F 125 MET cc_start: 0.9534 (ttt) cc_final: 0.9201 (ttt) REVERT: G 104 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8930 (tp) REVERT: G 166 TRP cc_start: 0.8559 (t60) cc_final: 0.8036 (t60) REVERT: G 180 ARG cc_start: 0.8223 (mtt180) cc_final: 0.7659 (mmt-90) REVERT: G 227 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.7530 (ttp80) REVERT: G 291 ASP cc_start: 0.8446 (m-30) cc_final: 0.8219 (m-30) REVERT: G 308 LYS cc_start: 0.8956 (mttt) cc_final: 0.8607 (mttm) REVERT: G 355 ASN cc_start: 0.8495 (p0) cc_final: 0.8280 (p0) REVERT: G 369 TRP cc_start: 0.9132 (t60) cc_final: 0.8691 (t60) REVERT: G 499 HIS cc_start: 0.8568 (m-70) cc_final: 0.8096 (p-80) REVERT: G 526 ASP cc_start: 0.9033 (t70) cc_final: 0.8327 (t70) REVERT: G 534 TYR cc_start: 0.8831 (t80) cc_final: 0.8358 (t80) REVERT: G 550 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8719 (ttp80) REVERT: H 9 GLN cc_start: 0.8871 (mp10) cc_final: 0.8598 (pm20) REVERT: H 12 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8463 (mm-30) REVERT: H 37 MET cc_start: 0.9430 (mmm) cc_final: 0.9217 (tpp) REVERT: H 52 MET cc_start: 0.9177 (mtm) cc_final: 0.8714 (mtm) REVERT: H 54 ASN cc_start: 0.9168 (m-40) cc_final: 0.8716 (m110) REVERT: H 56 VAL cc_start: 0.8894 (t) cc_final: 0.8620 (p) REVERT: H 72 MET cc_start: 0.9418 (ptm) cc_final: 0.9041 (tmm) REVERT: H 75 ARG cc_start: 0.8466 (ptt90) cc_final: 0.8231 (tmm-80) REVERT: H 112 ASN cc_start: 0.8692 (m-40) cc_final: 0.8265 (m110) REVERT: H 115 GLU cc_start: 0.8821 (mp0) cc_final: 0.7995 (mp0) REVERT: H 117 LEU cc_start: 0.8771 (mt) cc_final: 0.8309 (mt) REVERT: H 120 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8775 (mm-30) REVERT: H 121 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8573 (mm-30) REVERT: H 125 MET cc_start: 0.9533 (ttt) cc_final: 0.9198 (ttt) outliers start: 77 outliers final: 58 residues processed: 655 average time/residue: 0.1091 time to fit residues: 109.7816 Evaluate side-chains 699 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 634 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 135 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 513 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 A residue 550 ARG Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 92 VAL 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 167 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 550 ARG Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 92 VAL 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 190 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 92 VAL 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 167 SER Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 532 GLU Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 550 ARG Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 102 SER 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: 0.9990 chunk 5 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 119 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.092021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.075413 restraints weight = 38750.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.078153 restraints weight = 19421.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.080064 restraints weight = 12232.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.081415 restraints weight = 8739.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.082377 restraints weight = 6797.899| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15228 Z= 0.161 Angle : 0.630 11.506 20644 Z= 0.317 Chirality : 0.040 0.216 2368 Planarity : 0.004 0.036 2576 Dihedral : 3.532 18.573 2104 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 5.11 % Allowed : 29.49 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.30 (0.20), residues: 1904 helix: 2.94 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.05 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 127 TYR 0.020 0.001 TYR E 268 PHE 0.037 0.002 PHE E 341 TRP 0.008 0.001 TRP C 369 HIS 0.002 0.001 HIS G 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (15228) covalent geometry : angle 0.62998 / 0.32 (20644) hydrogen bonds : bond 0.03534 / 2.41 ( 1112) hydrogen bonds : angle 4.01824 / 3.01 ( 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 707 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 633 time to evaluate : 0.599 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 180 ARG cc_start: 0.8276 (mtt180) cc_final: 0.7648 (mtt-85) REVERT: A 227 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.7383 (ttp80) REVERT: A 291 ASP cc_start: 0.8437 (m-30) cc_final: 0.8223 (m-30) REVERT: A 308 LYS cc_start: 0.8949 (mttt) cc_final: 0.8616 (mttm) REVERT: A 369 TRP cc_start: 0.9161 (t60) cc_final: 0.8701 (t60) REVERT: A 499 HIS cc_start: 0.8581 (m-70) cc_final: 0.8120 (p-80) REVERT: A 526 ASP cc_start: 0.9046 (t70) cc_final: 0.8357 (t70) REVERT: A 533 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8487 (tm-30) REVERT: B 9 GLN cc_start: 0.8848 (mp10) cc_final: 0.8564 (pm20) REVERT: B 12 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8488 (mm-30) REVERT: B 37 MET cc_start: 0.9388 (mmm) cc_final: 0.9057 (mmm) REVERT: B 52 MET cc_start: 0.9170 (mtm) cc_final: 0.8727 (mtm) REVERT: B 54 ASN cc_start: 0.9192 (m-40) cc_final: 0.8765 (m110) REVERT: B 72 MET cc_start: 0.9426 (ptm) cc_final: 0.9086 (tmm) REVERT: B 91 ARG cc_start: 0.8675 (ttm-80) cc_final: 0.8461 (ttm110) REVERT: B 112 ASN cc_start: 0.8677 (m-40) cc_final: 0.8215 (m110) REVERT: B 115 GLU cc_start: 0.8810 (mp0) cc_final: 0.7956 (mp0) REVERT: B 117 LEU cc_start: 0.8742 (mt) cc_final: 0.8439 (mt) REVERT: B 121 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8579 (mm-30) REVERT: B 125 MET cc_start: 0.9528 (ttt) cc_final: 0.9192 (ttt) REVERT: C 104 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8979 (tp) REVERT: C 166 TRP cc_start: 0.8590 (t60) cc_final: 0.8074 (t60) REVERT: C 180 ARG cc_start: 0.8263 (mtt180) cc_final: 0.7627 (mtt-85) REVERT: C 291 ASP cc_start: 0.8455 (m-30) cc_final: 0.8227 (m-30) REVERT: C 308 LYS cc_start: 0.8967 (mttt) cc_final: 0.8620 (mttm) REVERT: C 369 TRP cc_start: 0.9151 (t60) cc_final: 0.8685 (t60) REVERT: C 499 HIS cc_start: 0.8578 (m-70) cc_final: 0.8116 (p-80) REVERT: C 526 ASP cc_start: 0.9047 (t70) cc_final: 0.8354 (t70) REVERT: C 534 TYR cc_start: 0.8780 (t80) cc_final: 0.8195 (t80) REVERT: C 550 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8903 (mtp-110) REVERT: D 9 GLN cc_start: 0.8847 (mp10) cc_final: 0.8564 (pm20) REVERT: D 12 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8501 (mm-30) REVERT: D 37 MET cc_start: 0.9386 (mmm) cc_final: 0.9056 (mmm) REVERT: D 52 MET cc_start: 0.9172 (mtm) cc_final: 0.8725 (mtm) REVERT: D 54 ASN cc_start: 0.9192 (m-40) cc_final: 0.8766 (m110) REVERT: D 72 MET cc_start: 0.9425 (ptm) cc_final: 0.9084 (tmm) REVERT: D 115 GLU cc_start: 0.8812 (mp0) cc_final: 0.7962 (mp0) REVERT: D 117 LEU cc_start: 0.8694 (mt) cc_final: 0.8374 (mt) REVERT: D 120 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8777 (mm-30) REVERT: D 121 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8581 (mm-30) REVERT: D 125 MET cc_start: 0.9519 (ttt) cc_final: 0.9185 (ttt) REVERT: E 180 ARG cc_start: 0.8281 (mtt180) cc_final: 0.7677 (mtt-85) REVERT: E 227 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.7404 (ttp80) REVERT: E 291 ASP cc_start: 0.8437 (m-30) cc_final: 0.8221 (m-30) REVERT: E 308 LYS cc_start: 0.8957 (mttt) cc_final: 0.8623 (mttm) REVERT: E 369 TRP cc_start: 0.9145 (t60) cc_final: 0.8698 (t60) REVERT: E 499 HIS cc_start: 0.8571 (m-70) cc_final: 0.8110 (p-80) REVERT: E 526 ASP cc_start: 0.9053 (t70) cc_final: 0.8364 (t70) REVERT: E 534 TYR cc_start: 0.8777 (t80) cc_final: 0.8028 (t80) REVERT: F 9 GLN cc_start: 0.8845 (mp10) cc_final: 0.8562 (pm20) REVERT: F 12 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8497 (mm-30) REVERT: F 37 MET cc_start: 0.9435 (mmm) cc_final: 0.9062 (mmm) REVERT: F 52 MET cc_start: 0.9196 (mtm) cc_final: 0.8729 (mtm) REVERT: F 54 ASN cc_start: 0.9187 (m-40) cc_final: 0.8725 (m110) REVERT: F 72 MET cc_start: 0.9419 (ptm) cc_final: 0.9089 (tmm) REVERT: F 112 ASN cc_start: 0.8691 (m-40) cc_final: 0.8228 (m110) REVERT: F 115 GLU cc_start: 0.8810 (mp0) cc_final: 0.7961 (mp0) REVERT: F 117 LEU cc_start: 0.8692 (mt) cc_final: 0.8373 (mt) REVERT: F 120 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8780 (mm-30) REVERT: F 121 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8589 (mm-30) REVERT: F 125 MET cc_start: 0.9528 (ttt) cc_final: 0.9192 (ttt) REVERT: G 104 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8966 (tp) REVERT: G 166 TRP cc_start: 0.8562 (t60) cc_final: 0.8050 (t60) REVERT: G 180 ARG cc_start: 0.8261 (mtt180) cc_final: 0.7624 (mtt-85) REVERT: G 227 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.7511 (ttp80) REVERT: G 291 ASP cc_start: 0.8458 (m-30) cc_final: 0.8228 (m-30) REVERT: G 308 LYS cc_start: 0.8975 (mttt) cc_final: 0.8626 (mttm) REVERT: G 369 TRP cc_start: 0.9149 (t60) cc_final: 0.8694 (t60) REVERT: G 499 HIS cc_start: 0.8581 (m-70) cc_final: 0.8121 (p-80) REVERT: G 526 ASP cc_start: 0.9051 (t70) cc_final: 0.8356 (t70) REVERT: G 534 TYR cc_start: 0.8771 (t80) cc_final: 0.8169 (t80) REVERT: H 9 GLN cc_start: 0.8845 (mp10) cc_final: 0.8582 (pm20) REVERT: H 12 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8440 (mm-30) REVERT: H 37 MET cc_start: 0.9391 (mmm) cc_final: 0.9058 (mmm) REVERT: H 46 GLU cc_start: 0.9192 (tp30) cc_final: 0.8919 (tp30) REVERT: H 52 MET cc_start: 0.9151 (mtm) cc_final: 0.8713 (mtm) REVERT: H 54 ASN cc_start: 0.9172 (m-40) cc_final: 0.8710 (m110) REVERT: H 56 VAL cc_start: 0.8931 (t) cc_final: 0.8723 (p) REVERT: H 72 MET cc_start: 0.9405 (ptm) cc_final: 0.8925 (tmm) REVERT: H 75 ARG cc_start: 0.8414 (ptt90) cc_final: 0.7782 (tmm-80) REVERT: H 112 ASN cc_start: 0.8727 (m-40) cc_final: 0.8286 (m110) REVERT: H 115 GLU cc_start: 0.8811 (mp0) cc_final: 0.7961 (mp0) REVERT: H 117 LEU cc_start: 0.8696 (mt) cc_final: 0.8378 (mt) REVERT: H 120 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8777 (mm-30) REVERT: H 121 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8582 (mm-30) REVERT: H 125 MET cc_start: 0.9525 (ttt) cc_final: 0.9186 (ttt) outliers start: 74 outliers final: 63 residues processed: 659 average time/residue: 0.1128 time to fit residues: 114.2846 Evaluate side-chains 698 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 629 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 135 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 ILE 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 513 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 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 92 VAL 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 114 VAL Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 254 THR 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 C residue 550 ARG Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 92 VAL 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 167 SER Chi-restraints excluded: chain E residue 190 VAL 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 513 VAL Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 92 VAL 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 114 VAL Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 254 THR 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 92 VAL Chi-restraints excluded: chain H residue 102 SER 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: 0.9990 chunk 44 optimal weight: 0.9990 chunk 30 optimal weight: 0.0270 chunk 128 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 20 optimal weight: 0.0870 chunk 77 optimal weight: 0.9980 chunk 175 optimal weight: 0.6980 chunk 171 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.093827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.076959 restraints weight = 38189.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.079713 restraints weight = 19147.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.081627 restraints weight = 12113.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.083028 restraints weight = 8701.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.084009 restraints weight = 6767.532| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15228 Z= 0.133 Angle : 0.632 11.828 20644 Z= 0.311 Chirality : 0.040 0.230 2368 Planarity : 0.004 0.035 2576 Dihedral : 3.489 18.065 2104 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.11 % Allowed : 31.56 % Favored : 65.33 % 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: 3.24 (0.20), residues: 1904 helix: 2.87 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.99 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 127 TYR 0.038 0.001 TYR G 161 PHE 0.029 0.001 PHE E 341 TRP 0.008 0.001 TRP G 295 HIS 0.003 0.000 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (15228) covalent geometry : angle 0.63168 / 0.31 (20644) hydrogen bonds : bond 0.03404 / 2.32 ( 1112) hydrogen bonds : angle 3.92190 / 2.94 ( 3336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2942.04 seconds wall clock time: 51 minutes 30.65 seconds (3090.65 seconds total)