Starting phenix.real_space_refine on Wed Jan 14 23:41:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8def_27392/01_2026/8def_27392.cif Found real_map, /net/cci-nas-00/data/ceres_data/8def_27392/01_2026/8def_27392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8def_27392/01_2026/8def_27392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8def_27392/01_2026/8def_27392.map" model { file = "/net/cci-nas-00/data/ceres_data/8def_27392/01_2026/8def_27392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8def_27392/01_2026/8def_27392.cif" } resolution = 4.2 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= -0.002 sd= 0.012 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: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 12845 2.51 5 N 3500 2.21 5 O 3852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20314 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2989 Classifications: {'peptide': 395} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 367} Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2611 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 20, 'TRANS': 310} Chain: "F" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2989 Classifications: {'peptide': 395} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 367} Chain: "G" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2611 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 20, 'TRANS': 310} Chain: "J" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2989 Classifications: {'peptide': 395} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 367} Chain: "K" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2611 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 20, 'TRANS': 310} Chain: "S" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 955 Classifications: {'peptide': 124} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 117} Chain: "T" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 97} Chain: "U" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 955 Classifications: {'peptide': 124} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 117} Chain: "V" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 97} Time building chain proxies: 4.86, per 1000 atoms: 0.24 Number of scatterers: 20314 At special positions: 0 Unit cell: (158.115, 160.605, 153.135, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 3852 8.00 N 3500 7.00 C 12845 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.06 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.06 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.05 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 28 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 108 " distance=2.04 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 204 " - pdb=" SG CYS B 229 " distance=2.03 Simple disulfide: pdb=" SG CYS B 206 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 114 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 94 " distance=2.04 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 96 " distance=2.05 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 271 " distance=2.06 Simple disulfide: pdb=" SG CYS F 301 " - pdb=" SG CYS F 376 " distance=2.04 Simple disulfide: pdb=" SG CYS F 306 " - pdb=" SG CYS F 380 " distance=2.03 Simple disulfide: pdb=" SG CYS F 328 " - pdb=" SG CYS F 370 " distance=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 127 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 28 " distance=2.02 Simple disulfide: pdb=" SG CYS G 94 " - pdb=" SG CYS G 108 " distance=2.03 Simple disulfide: pdb=" SG CYS G 155 " - pdb=" SG CYS G 269 " distance=2.03 Simple disulfide: pdb=" SG CYS G 204 " - pdb=" SG CYS G 229 " distance=2.03 Simple disulfide: pdb=" SG CYS G 206 " - pdb=" SG CYS G 223 " distance=2.03 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 94 " distance=2.03 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.06 Simple disulfide: pdb=" SG CYS J 259 " - pdb=" SG CYS J 271 " distance=2.06 Simple disulfide: pdb=" SG CYS J 301 " - pdb=" SG CYS J 376 " distance=2.05 Simple disulfide: pdb=" SG CYS J 306 " - pdb=" SG CYS J 380 " distance=2.03 Simple disulfide: pdb=" SG CYS J 328 " - pdb=" SG CYS J 370 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 127 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 28 " distance=2.03 Simple disulfide: pdb=" SG CYS K 94 " - pdb=" SG CYS K 108 " distance=2.03 Simple disulfide: pdb=" SG CYS K 155 " - pdb=" SG CYS K 269 " distance=2.03 Simple disulfide: pdb=" SG CYS K 204 " - pdb=" SG CYS K 229 " distance=2.03 Simple disulfide: pdb=" SG CYS K 206 " - pdb=" SG CYS K 223 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 97 " distance=2.03 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 87 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 97 " distance=2.03 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 87 " distance=2.03 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: 1.60 Conformation dependent library (CDL) restraints added in 972.9 milliseconds 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4874 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 70 sheets defined 3.6% alpha, 46.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'F' and resid 238 through 246 Processing helix chain 'F' and resid 250 through 254 removed outlier: 3.612A pdb=" N GLU F 253 " --> pdb=" O PRO F 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 227 No H-bonds generated for 'chain 'G' and resid 225 through 227' Processing helix chain 'J' and resid 238 through 246 Processing helix chain 'J' and resid 250 through 254 removed outlier: 3.504A pdb=" N GLU J 253 " --> pdb=" O PRO J 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 227 No H-bonds generated for 'chain 'K' and resid 225 through 227' Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.842A pdb=" N TYR S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 88 through 92 Processing helix chain 'T' and resid 26 through 30 Processing helix chain 'T' and resid 78 through 82 Processing helix chain 'U' and resid 28 through 32 removed outlier: 3.826A pdb=" N TYR U 32 " --> pdb=" O PHE U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 88 through 92 Processing helix chain 'V' and resid 26 through 30 Processing helix chain 'V' and resid 78 through 82 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 8 removed outlier: 4.016A pdb=" N LYS A 160 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 5.621A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 19 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 48 removed outlier: 6.330A pdb=" N LYS A 44 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LYS A 123 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR A 46 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA6, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.016A pdb=" N VAL A 108 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ASP A 75 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA8, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA9, first strand: chain 'A' and resid 296 through 303 Processing sheet with id=AB1, first strand: chain 'A' and resid 330 through 332 Processing sheet with id=AB2, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=AB3, first strand: chain 'B' and resid 34 through 38 removed outlier: 9.241A pdb=" N ILE B 34 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N SER B 51 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN B 36 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 10.342A pdb=" N ILE B 48 " --> pdb=" O GLN B 107 " (cutoff:3.500A) removed outlier: 11.181A pdb=" N GLN B 107 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 11.573A pdb=" N VAL B 50 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 10.848A pdb=" N LEU B 105 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N ALA B 52 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE B 103 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE B 88 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ARG B 96 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 11.414A pdb=" N ILE B 86 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP B 112 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 66 through 70 Processing sheet with id=AB5, first strand: chain 'B' and resid 151 through 158 Processing sheet with id=AB6, first strand: chain 'B' and resid 240 through 241 Processing sheet with id=AB7, first strand: chain 'B' and resid 183 through 185 removed outlier: 4.452A pdb=" N VAL B 190 " --> pdb=" O MET B 220 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 209 through 214 Processing sheet with id=AB9, first strand: chain 'B' and resid 278 through 282 removed outlier: 7.098A pdb=" N LEU B 288 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N PHE B 322 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU B 290 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ARG B 320 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ALA B 292 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR B 318 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ARG B 294 " --> pdb=" O GLY B 316 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLY B 316 " --> pdb=" O ARG B 294 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 278 through 282 Processing sheet with id=AC2, first strand: chain 'F' and resid 2 through 8 removed outlier: 3.913A pdb=" N LYS F 160 " --> pdb=" O ASP F 281 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 15 through 19 removed outlier: 5.639A pdb=" N ILE F 31 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL F 136 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL F 33 " --> pdb=" O ARG F 134 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG F 134 " --> pdb=" O VAL F 33 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 15 through 19 Processing sheet with id=AC5, first strand: chain 'F' and resid 43 through 48 removed outlier: 6.173A pdb=" N LYS F 44 " --> pdb=" O LYS F 123 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS F 123 " --> pdb=" O LYS F 44 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR F 46 " --> pdb=" O ALA F 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.635A pdb=" N GLN F 59 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 51 through 54 removed outlier: 5.258A pdb=" N VAL F 108 " --> pdb=" O ASP F 75 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASP F 75 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 203 through 204 Processing sheet with id=AC9, first strand: chain 'F' and resid 220 through 221 Processing sheet with id=AD1, first strand: chain 'F' and resid 296 through 303 Processing sheet with id=AD2, first strand: chain 'F' and resid 330 through 332 Processing sheet with id=AD3, first strand: chain 'G' and resid 17 through 19 Processing sheet with id=AD4, first strand: chain 'G' and resid 36 through 38 removed outlier: 3.758A pdb=" N ASN G 36 " --> pdb=" O GLN G 49 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR G 102 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ALA G 52 " --> pdb=" O LYS G 100 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LYS G 100 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N PHE G 54 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N GLY G 98 " --> pdb=" O PHE G 54 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 66 through 70 Processing sheet with id=AD6, first strand: chain 'G' and resid 86 through 89 removed outlier: 5.542A pdb=" N LYS G 131 " --> pdb=" O SER G 113 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N THR G 115 " --> pdb=" O VAL G 129 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL G 129 " --> pdb=" O THR G 115 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N SER G 117 " --> pdb=" O CYS G 127 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N CYS G 127 " --> pdb=" O SER G 117 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N THR G 119 " --> pdb=" O ASN G 125 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ASN G 125 " --> pdb=" O THR G 119 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 151 through 158 Processing sheet with id=AD8, first strand: chain 'G' and resid 240 through 241 Processing sheet with id=AD9, first strand: chain 'G' and resid 183 through 185 removed outlier: 4.428A pdb=" N VAL G 190 " --> pdb=" O MET G 220 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 209 through 214 Processing sheet with id=AE2, first strand: chain 'G' and resid 278 through 282 removed outlier: 7.051A pdb=" N LEU G 288 " --> pdb=" O PHE G 322 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N PHE G 322 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU G 290 " --> pdb=" O ARG G 320 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ARG G 320 " --> pdb=" O LEU G 290 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ALA G 292 " --> pdb=" O THR G 318 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N THR G 318 " --> pdb=" O ALA G 292 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG G 294 " --> pdb=" O GLY G 316 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLY G 316 " --> pdb=" O ARG G 294 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 278 through 282 Processing sheet with id=AE4, first strand: chain 'J' and resid 2 through 8 removed outlier: 4.257A pdb=" N LYS J 160 " --> pdb=" O ASP J 281 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 15 through 21 removed outlier: 5.016A pdb=" N ARG J 21 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ALA J 25 " --> pdb=" O ARG J 21 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ILE J 31 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N VAL J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N VAL J 33 " --> pdb=" O ARG J 134 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG J 134 " --> pdb=" O VAL J 33 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 15 through 21 removed outlier: 5.016A pdb=" N ARG J 21 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ALA J 25 " --> pdb=" O ARG J 21 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 43 through 48 removed outlier: 6.217A pdb=" N LYS J 44 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS J 123 " --> pdb=" O LYS J 44 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR J 46 " --> pdb=" O ALA J 121 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 51 through 54 Processing sheet with id=AE9, first strand: chain 'J' and resid 51 through 54 removed outlier: 5.322A pdb=" N VAL J 108 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ASP J 75 " --> pdb=" O VAL J 108 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 203 through 204 Processing sheet with id=AF2, first strand: chain 'J' and resid 220 through 221 Processing sheet with id=AF3, first strand: chain 'J' and resid 296 through 303 Processing sheet with id=AF4, first strand: chain 'J' and resid 330 through 332 Processing sheet with id=AF5, first strand: chain 'K' and resid 17 through 19 Processing sheet with id=AF6, first strand: chain 'K' and resid 34 through 38 removed outlier: 9.354A pdb=" N ILE K 34 " --> pdb=" O SER K 51 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N SER K 51 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN K 36 " --> pdb=" O GLN K 49 " (cutoff:3.500A) removed outlier: 11.449A pdb=" N ILE K 48 " --> pdb=" O GLN K 107 " (cutoff:3.500A) removed outlier: 11.179A pdb=" N GLN K 107 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 11.694A pdb=" N VAL K 50 " --> pdb=" O LEU K 105 " (cutoff:3.500A) removed outlier: 11.094A pdb=" N LEU K 105 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N ALA K 52 " --> pdb=" O PHE K 103 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N PHE K 103 " --> pdb=" O ALA K 52 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE K 88 " --> pdb=" O CYS K 94 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ARG K 96 " --> pdb=" O ILE K 86 " (cutoff:3.500A) removed outlier: 11.291A pdb=" N ILE K 86 " --> pdb=" O ARG K 96 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP K 112 " --> pdb=" O LYS K 131 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 66 through 70 Processing sheet with id=AF8, first strand: chain 'K' and resid 151 through 158 Processing sheet with id=AF9, first strand: chain 'K' and resid 240 through 241 Processing sheet with id=AG1, first strand: chain 'K' and resid 183 through 185 Processing sheet with id=AG2, first strand: chain 'K' and resid 209 through 214 Processing sheet with id=AG3, first strand: chain 'K' and resid 278 through 282 removed outlier: 5.208A pdb=" N ARG K 294 " --> pdb=" O ILE K 314 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE K 314 " --> pdb=" O ARG K 294 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N THR K 296 " --> pdb=" O GLU K 312 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU K 312 " --> pdb=" O THR K 296 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU K 298 " --> pdb=" O THR K 310 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR K 310 " --> pdb=" O LEU K 298 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 278 through 282 Processing sheet with id=AG5, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AG6, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.193A pdb=" N GLY S 10 " --> pdb=" O THR S 121 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG S 33 " --> pdb=" O VAL S 100 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N MET S 34 " --> pdb=" O THR S 50 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.193A pdb=" N GLY S 10 " --> pdb=" O THR S 121 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N CYS S 97 " --> pdb=" O TRP S 114 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TRP S 114 " --> pdb=" O CYS S 97 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ARG S 99 " --> pdb=" O ASP S 112 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'T' and resid 18 through 23 Processing sheet with id=AG9, first strand: chain 'T' and resid 44 through 48 removed outlier: 6.279A pdb=" N TRP T 34 " --> pdb=" O VAL T 46 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'T' and resid 44 through 48 removed outlier: 6.279A pdb=" N TRP T 34 " --> pdb=" O VAL T 46 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'U' and resid 3 through 7 Processing sheet with id=AH3, first strand: chain 'U' and resid 11 through 12 removed outlier: 4.011A pdb=" N ARG U 33 " --> pdb=" O VAL U 100 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N MET U 34 " --> pdb=" O THR U 50 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N THR U 50 " --> pdb=" O MET U 34 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP U 36 " --> pdb=" O VAL U 48 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'U' and resid 11 through 12 removed outlier: 3.674A pdb=" N ALA U 108 " --> pdb=" O GLU U 103 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'V' and resid 18 through 23 Processing sheet with id=AH6, first strand: chain 'V' and resid 44 through 48 removed outlier: 6.311A pdb=" N TRP V 34 " --> pdb=" O VAL V 46 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'V' and resid 44 through 48 removed outlier: 6.311A pdb=" N TRP V 34 " --> pdb=" O VAL V 46 " (cutoff:3.500A) 741 hydrogen bonds defined for protein. 1797 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.91 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6568 1.34 - 1.47: 5164 1.47 - 1.59: 8980 1.59 - 1.72: 0 1.72 - 1.85: 142 Bond restraints: 20854 Sorted by residual: bond pdb=" C SER K 25 " pdb=" N ALA K 26 " ideal model delta sigma weight residual 1.323 1.372 -0.049 1.64e-02 3.72e+03 8.96e+00 bond pdb=" C SER G 25 " pdb=" N ALA G 26 " ideal model delta sigma weight residual 1.331 1.386 -0.055 2.07e-02 2.33e+03 7.15e+00 bond pdb=" C LEU G 264 " pdb=" N THR G 265 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.86e-02 1.22e+03 6.34e+00 bond pdb=" C LEU K 264 " pdb=" N THR K 265 " ideal model delta sigma weight residual 1.329 1.401 -0.072 3.03e-02 1.09e+03 5.62e+00 bond pdb=" C THR F 39 " pdb=" N PRO F 40 " ideal model delta sigma weight residual 1.328 1.355 -0.027 1.25e-02 6.40e+03 4.59e+00 ... (remaining 20849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 27501 2.08 - 4.16: 757 4.16 - 6.24: 122 6.24 - 8.32: 8 8.32 - 10.40: 10 Bond angle restraints: 28398 Sorted by residual: angle pdb=" C ILE J 55 " pdb=" CA ILE J 55 " pdb=" CB ILE J 55 " ideal model delta sigma weight residual 111.08 115.78 -4.70 9.50e-01 1.11e+00 2.45e+01 angle pdb=" CA CYS A 62 " pdb=" CB CYS A 62 " pdb=" SG CYS A 62 " ideal model delta sigma weight residual 114.40 124.80 -10.40 2.30e+00 1.89e-01 2.04e+01 angle pdb=" CA CYS J 259 " pdb=" CB CYS J 259 " pdb=" SG CYS J 259 " ideal model delta sigma weight residual 114.40 124.74 -10.34 2.30e+00 1.89e-01 2.02e+01 angle pdb=" CA CYS J 63 " pdb=" CB CYS J 63 " pdb=" SG CYS J 63 " ideal model delta sigma weight residual 114.40 124.65 -10.25 2.30e+00 1.89e-01 1.98e+01 angle pdb=" CA CYS F 259 " pdb=" CB CYS F 259 " pdb=" SG CYS F 259 " ideal model delta sigma weight residual 114.40 124.46 -10.06 2.30e+00 1.89e-01 1.91e+01 ... (remaining 28393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 11196 15.61 - 31.23: 1001 31.23 - 46.84: 237 46.84 - 62.45: 58 62.45 - 78.07: 14 Dihedral angle restraints: 12506 sinusoidal: 4890 harmonic: 7616 Sorted by residual: dihedral pdb=" CB CYS J 259 " pdb=" SG CYS J 259 " pdb=" SG CYS J 271 " pdb=" CB CYS J 271 " ideal model delta sinusoidal sigma weight residual -86.00 -20.91 -65.09 1 1.00e+01 1.00e-02 5.56e+01 dihedral pdb=" CB CYS B 94 " pdb=" SG CYS B 94 " pdb=" SG CYS B 108 " pdb=" CB CYS B 108 " ideal model delta sinusoidal sigma weight residual 93.00 31.94 61.06 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CB CYS F 259 " pdb=" SG CYS F 259 " pdb=" SG CYS F 271 " pdb=" CB CYS F 271 " ideal model delta sinusoidal sigma weight residual -86.00 -26.78 -59.22 1 1.00e+01 1.00e-02 4.69e+01 ... (remaining 12503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2357 0.051 - 0.102: 599 0.102 - 0.153: 179 0.153 - 0.204: 20 0.204 - 0.255: 6 Chirality restraints: 3161 Sorted by residual: chirality pdb=" CA CYS J 63 " pdb=" N CYS J 63 " pdb=" C CYS J 63 " pdb=" CB CYS J 63 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA ILE A 31 " pdb=" N ILE A 31 " pdb=" C ILE A 31 " pdb=" CB ILE A 31 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILE V 92 " pdb=" CA ILE V 92 " pdb=" CG1 ILE V 92 " pdb=" CG2 ILE V 92 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 3158 not shown) Planarity restraints: 3657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 276 " 0.052 5.00e-02 4.00e+02 7.84e-02 9.84e+00 pdb=" N PRO B 277 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 277 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 277 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE T 100 " 0.021 2.00e-02 2.50e+03 2.26e-02 8.92e+00 pdb=" CG PHE T 100 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE T 100 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE T 100 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE T 100 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE T 100 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE T 100 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 100 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" CG ASN A 100 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A 100 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN A 100 " 0.013 2.00e-02 2.50e+03 ... (remaining 3654 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 593 2.67 - 3.23: 19956 3.23 - 3.79: 32844 3.79 - 4.34: 44542 4.34 - 4.90: 72230 Nonbonded interactions: 170165 Sorted by model distance: nonbonded pdb=" NH2 ARG U 38 " pdb=" O GLU U 90 " model vdw 2.117 3.120 nonbonded pdb=" O PRO K 31 " pdb=" OG SER K 51 " model vdw 2.120 3.040 nonbonded pdb=" OE1 GLU G 203 " pdb=" OH TYR G 209 " model vdw 2.134 3.040 nonbonded pdb=" O ILE B 86 " pdb=" NH2 ARG B 96 " model vdw 2.151 3.120 nonbonded pdb=" NZ LYS G 154 " pdb=" O CYS G 155 " model vdw 2.153 3.120 ... (remaining 170160 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'T' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 35.780 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.690 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 : 0.005 0.072 20897 Z= 0.201 Angle : 0.855 11.142 28484 Z= 0.457 Chirality : 0.052 0.255 3161 Planarity : 0.006 0.078 3657 Dihedral : 12.599 78.067 7503 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.30 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.35 (0.16), residues: 2618 helix: -1.08 (0.68), residues: 45 sheet: -0.89 (0.15), residues: 1125 loop : -0.81 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 306 TYR 0.036 0.002 TYR G 21 PHE 0.050 0.002 PHE T 100 TRP 0.021 0.001 TRP G 282 HIS 0.010 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00449 (20854) covalent geometry : angle 0.84333 (28398) SS BOND : bond 0.01043 ( 43) SS BOND : angle 2.71684 ( 86) hydrogen bonds : bond 0.11495 ( 666) hydrogen bonds : angle 7.45215 ( 1797) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 516 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8658 (mt) cc_final: 0.8218 (mt) REVERT: A 79 ARG cc_start: 0.8583 (ptm-80) cc_final: 0.8223 (ptm-80) REVERT: A 104 SER cc_start: 0.9265 (t) cc_final: 0.8784 (p) REVERT: A 174 ASP cc_start: 0.9006 (m-30) cc_final: 0.8450 (m-30) REVERT: A 186 ASN cc_start: 0.7142 (m-40) cc_final: 0.6874 (m-40) REVERT: B 61 THR cc_start: 0.9159 (m) cc_final: 0.8957 (p) REVERT: B 220 MET cc_start: 0.6213 (mtp) cc_final: 0.5855 (mtp) REVERT: F 15 TYR cc_start: 0.8272 (t80) cc_final: 0.7926 (t80) REVERT: F 99 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7312 (tm-30) REVERT: F 148 VAL cc_start: 0.9325 (t) cc_final: 0.9052 (t) REVERT: F 218 ASP cc_start: 0.8363 (t0) cc_final: 0.8031 (t70) REVERT: F 238 SER cc_start: 0.9251 (t) cc_final: 0.8820 (p) REVERT: F 251 LEU cc_start: 0.9053 (mm) cc_final: 0.8834 (mm) REVERT: F 273 TYR cc_start: 0.8261 (p90) cc_final: 0.7900 (p90) REVERT: G 21 TYR cc_start: 0.6942 (m-80) cc_final: 0.6460 (m-10) REVERT: G 49 GLN cc_start: 0.8428 (tt0) cc_final: 0.8210 (tt0) REVERT: G 169 ILE cc_start: 0.8831 (mm) cc_final: 0.8600 (tt) REVERT: G 241 PHE cc_start: 0.9186 (t80) cc_final: 0.8922 (t80) REVERT: G 280 THR cc_start: 0.8035 (m) cc_final: 0.7333 (p) REVERT: J 24 TYR cc_start: 0.6757 (m-80) cc_final: 0.6269 (m-80) REVERT: J 187 TYR cc_start: 0.8614 (t80) cc_final: 0.7735 (t80) REVERT: J 228 ASN cc_start: 0.8426 (m110) cc_final: 0.8126 (m110) REVERT: K 50 VAL cc_start: 0.8183 (m) cc_final: 0.7742 (p) REVERT: K 83 MET cc_start: 0.6285 (mmp) cc_final: 0.5539 (mmp) REVERT: K 157 VAL cc_start: 0.9537 (t) cc_final: 0.9190 (p) REVERT: K 280 THR cc_start: 0.8819 (m) cc_final: 0.8461 (p) REVERT: K 297 LEU cc_start: 0.9224 (tp) cc_final: 0.9008 (tp) REVERT: K 333 TRP cc_start: 0.8215 (t-100) cc_final: 0.7905 (t-100) REVERT: S 36 TRP cc_start: 0.7183 (m100) cc_final: 0.6515 (m100) REVERT: S 77 LYS cc_start: 0.9120 (pttm) cc_final: 0.8667 (pttm) REVERT: S 80 LEU cc_start: 0.8797 (tp) cc_final: 0.8355 (tp) REVERT: S 102 THR cc_start: 0.7622 (p) cc_final: 0.6754 (p) REVERT: T 31 LEU cc_start: 0.8656 (mp) cc_final: 0.8198 (mm) REVERT: T 72 LEU cc_start: 0.9030 (tp) cc_final: 0.8633 (tp) REVERT: T 85 TYR cc_start: 0.8142 (m-80) cc_final: 0.7298 (m-10) REVERT: U 29 PHE cc_start: 0.8357 (t80) cc_final: 0.7901 (t80) REVERT: U 45 LEU cc_start: 0.8646 (mm) cc_final: 0.8216 (mm) REVERT: U 46 GLU cc_start: 0.6989 (pm20) cc_final: 0.6109 (mp0) REVERT: U 79 THR cc_start: 0.7123 (m) cc_final: 0.5967 (m) REVERT: U 80 LEU cc_start: 0.9153 (tp) cc_final: 0.8753 (tp) REVERT: U 81 TYR cc_start: 0.8663 (m-80) cc_final: 0.8343 (m-80) REVERT: U 92 THR cc_start: 0.7447 (m) cc_final: 0.7118 (m) REVERT: V 34 TRP cc_start: 0.8206 (m100) cc_final: 0.7896 (m100) REVERT: V 47 ILE cc_start: 0.8358 (mm) cc_final: 0.7534 (mm) REVERT: V 95 ASP cc_start: 0.6244 (t0) cc_final: 0.5888 (t0) outliers start: 0 outliers final: 0 residues processed: 516 average time/residue: 0.1511 time to fit residues: 119.1508 Evaluate side-chains 368 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 258 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 289 HIS G 336 HIS ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 228 ASN K 49 GLN K 177 HIS T 96 HIS V 36 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.084755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.066463 restraints weight = 89399.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.068458 restraints weight = 47009.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.069782 restraints weight = 29842.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.070661 restraints weight = 21537.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.071184 restraints weight = 17122.131| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 20897 Z= 0.200 Angle : 0.685 7.663 28484 Z= 0.362 Chirality : 0.047 0.171 3161 Planarity : 0.005 0.052 3657 Dihedral : 5.893 30.186 2856 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.18 % Allowed : 4.60 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.21 (0.16), residues: 2618 helix: -0.87 (0.74), residues: 45 sheet: -0.79 (0.15), residues: 1117 loop : -0.73 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG G 23 TYR 0.024 0.002 TYR J 46 PHE 0.030 0.002 PHE U 69 TRP 0.017 0.002 TRP G 282 HIS 0.008 0.001 HIS T 96 Details of bonding type rmsd covalent geometry : bond 0.00446 (20854) covalent geometry : angle 0.67896 (28398) SS BOND : bond 0.00356 ( 43) SS BOND : angle 1.84781 ( 86) hydrogen bonds : bond 0.03596 ( 666) hydrogen bonds : angle 6.23220 ( 1797) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 454 time to evaluate : 0.810 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: A 29 LEU cc_start: 0.8760 (mt) cc_final: 0.8395 (mt) REVERT: A 79 ARG cc_start: 0.8787 (ptm-80) cc_final: 0.8452 (ptm-80) REVERT: A 104 SER cc_start: 0.9431 (t) cc_final: 0.8865 (p) REVERT: A 174 ASP cc_start: 0.9157 (m-30) cc_final: 0.8465 (m-30) REVERT: A 186 ASN cc_start: 0.8062 (m-40) cc_final: 0.7078 (m-40) REVERT: A 257 PHE cc_start: 0.9008 (m-10) cc_final: 0.8781 (m-10) REVERT: A 339 LEU cc_start: 0.8764 (tp) cc_final: 0.8542 (tp) REVERT: B 40 GLU cc_start: 0.8651 (mp0) cc_final: 0.8052 (mp0) REVERT: B 42 ASP cc_start: 0.8118 (m-30) cc_final: 0.7867 (m-30) REVERT: B 103 PHE cc_start: 0.8581 (m-10) cc_final: 0.8284 (m-10) REVERT: B 220 MET cc_start: 0.6507 (mtp) cc_final: 0.6190 (mtp) REVERT: B 297 LEU cc_start: 0.9535 (tp) cc_final: 0.9242 (tp) REVERT: F 99 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7343 (tm-30) REVERT: F 103 LEU cc_start: 0.8827 (mt) cc_final: 0.8543 (mt) REVERT: F 196 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8671 (mmmm) REVERT: F 251 LEU cc_start: 0.9173 (mm) cc_final: 0.8952 (mm) REVERT: F 334 SER cc_start: 0.8800 (t) cc_final: 0.8589 (t) REVERT: G 21 TYR cc_start: 0.7372 (m-80) cc_final: 0.6801 (m-80) REVERT: G 43 ASP cc_start: 0.8919 (p0) cc_final: 0.8630 (p0) REVERT: G 241 PHE cc_start: 0.9427 (t80) cc_final: 0.9175 (t80) REVERT: G 280 THR cc_start: 0.8345 (m) cc_final: 0.7838 (p) REVERT: G 291 THR cc_start: 0.9443 (m) cc_final: 0.9171 (p) REVERT: J 18 LEU cc_start: 0.8735 (tp) cc_final: 0.8451 (tp) REVERT: J 108 VAL cc_start: 0.9162 (m) cc_final: 0.8787 (p) REVERT: J 251 LEU cc_start: 0.9271 (mm) cc_final: 0.9029 (mm) REVERT: J 311 ASP cc_start: 0.9247 (p0) cc_final: 0.8860 (p0) REVERT: K 36 ASN cc_start: 0.8851 (t0) cc_final: 0.7689 (t0) REVERT: K 57 ASN cc_start: 0.9086 (p0) cc_final: 0.8851 (p0) REVERT: K 70 MET cc_start: 0.7890 (tpt) cc_final: 0.7509 (tpt) REVERT: K 107 GLN cc_start: 0.8551 (tt0) cc_final: 0.8175 (pt0) REVERT: K 144 LEU cc_start: 0.8940 (tp) cc_final: 0.7674 (tp) REVERT: K 157 VAL cc_start: 0.9362 (t) cc_final: 0.9048 (p) REVERT: K 241 PHE cc_start: 0.9061 (t80) cc_final: 0.8805 (t80) REVERT: K 297 LEU cc_start: 0.9046 (tp) cc_final: 0.8778 (tp) REVERT: K 322 PHE cc_start: 0.9046 (m-80) cc_final: 0.8702 (m-80) REVERT: S 4 LEU cc_start: 0.8093 (mt) cc_final: 0.7753 (mm) REVERT: S 36 TRP cc_start: 0.7047 (m100) cc_final: 0.6354 (m100) REVERT: S 59 THR cc_start: 0.8616 (p) cc_final: 0.8317 (t) REVERT: S 77 LYS cc_start: 0.8928 (pttm) cc_final: 0.8557 (pttm) REVERT: S 80 LEU cc_start: 0.8847 (tp) cc_final: 0.8294 (tp) REVERT: S 82 LEU cc_start: 0.8247 (tp) cc_final: 0.7997 (tp) REVERT: S 101 VAL cc_start: 0.8947 (p) cc_final: 0.8598 (m) REVERT: T 26 ASN cc_start: 0.8790 (t0) cc_final: 0.8189 (t0) REVERT: T 85 TYR cc_start: 0.8080 (m-80) cc_final: 0.7438 (m-10) REVERT: T 106 LEU cc_start: 0.8843 (mm) cc_final: 0.7933 (mm) REVERT: U 29 PHE cc_start: 0.8200 (t80) cc_final: 0.7925 (t80) REVERT: U 32 TYR cc_start: 0.8409 (m-80) cc_final: 0.8134 (m-10) REVERT: U 33 ARG cc_start: 0.8577 (ttm110) cc_final: 0.7893 (ttp-110) REVERT: U 38 ARG cc_start: 0.8833 (ttp-170) cc_final: 0.8301 (ttp-170) REVERT: U 74 ASP cc_start: 0.8788 (t70) cc_final: 0.8555 (t0) REVERT: U 80 LEU cc_start: 0.9232 (tp) cc_final: 0.8799 (tp) REVERT: U 81 TYR cc_start: 0.8735 (m-80) cc_final: 0.8385 (m-10) REVERT: U 100 VAL cc_start: 0.7977 (t) cc_final: 0.7270 (t) REVERT: V 2 TYR cc_start: 0.7149 (m-10) cc_final: 0.6942 (m-80) REVERT: V 31 LEU cc_start: 0.8117 (mm) cc_final: 0.7827 (mm) REVERT: V 47 ILE cc_start: 0.8486 (mm) cc_final: 0.8181 (mm) REVERT: V 105 ARG cc_start: 0.8067 (mmm-85) cc_final: 0.7670 (mmm-85) outliers start: 4 outliers final: 2 residues processed: 458 average time/residue: 0.1503 time to fit residues: 105.9527 Evaluate side-chains 311 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 309 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 15 optimal weight: 0.9990 chunk 223 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 233 optimal weight: 0.0010 chunk 185 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 245 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 HIS ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN ** G 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 289 HIS J 230 HIS K 53 GLN K 289 HIS K 335 ASN T 41 GLN U 85 HIS ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.082852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.064421 restraints weight = 90272.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.066389 restraints weight = 47618.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.067685 restraints weight = 30395.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.068544 restraints weight = 22086.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.069114 restraints weight = 17685.168| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20897 Z= 0.194 Angle : 0.674 8.773 28484 Z= 0.354 Chirality : 0.046 0.166 3161 Planarity : 0.005 0.107 3657 Dihedral : 5.820 28.875 2856 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.13 % Allowed : 3.97 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.10 % 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: -1.22 (0.16), residues: 2618 helix: -0.72 (0.74), residues: 45 sheet: -0.83 (0.15), residues: 1170 loop : -0.68 (0.17), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG T 105 TYR 0.021 0.002 TYR F 107 PHE 0.024 0.002 PHE G 262 TRP 0.014 0.002 TRP G 282 HIS 0.007 0.001 HIS T 96 Details of bonding type rmsd covalent geometry : bond 0.00432 (20854) covalent geometry : angle 0.66431 (28398) SS BOND : bond 0.00422 ( 43) SS BOND : angle 2.14702 ( 86) hydrogen bonds : bond 0.03399 ( 666) hydrogen bonds : angle 6.03888 ( 1797) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 425 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8808 (mt) cc_final: 0.8452 (mt) REVERT: A 79 ARG cc_start: 0.8760 (ptm-80) cc_final: 0.8396 (ptm-80) REVERT: A 104 SER cc_start: 0.9470 (t) cc_final: 0.9029 (p) REVERT: A 195 MET cc_start: 0.8128 (mpp) cc_final: 0.7697 (mtt) REVERT: A 251 LEU cc_start: 0.9563 (mt) cc_final: 0.9275 (mp) REVERT: A 257 PHE cc_start: 0.9091 (m-10) cc_final: 0.8793 (m-10) REVERT: A 339 LEU cc_start: 0.8742 (tp) cc_final: 0.8485 (tp) REVERT: B 40 GLU cc_start: 0.8708 (mp0) cc_final: 0.8143 (mp0) REVERT: B 291 THR cc_start: 0.9196 (m) cc_final: 0.8880 (p) REVERT: B 297 LEU cc_start: 0.9592 (tp) cc_final: 0.9278 (tp) REVERT: F 99 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7406 (tm-30) REVERT: F 103 LEU cc_start: 0.8935 (mt) cc_final: 0.8694 (mt) REVERT: F 195 MET cc_start: 0.8517 (mpp) cc_final: 0.8033 (mpp) REVERT: F 196 LYS cc_start: 0.8976 (mmmt) cc_final: 0.8766 (mmmt) REVERT: F 390 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8277 (tm-30) REVERT: G 39 ASP cc_start: 0.8342 (p0) cc_final: 0.7971 (p0) REVERT: G 241 PHE cc_start: 0.9408 (t80) cc_final: 0.9165 (t80) REVERT: G 280 THR cc_start: 0.8655 (m) cc_final: 0.8239 (p) REVERT: G 291 THR cc_start: 0.9468 (m) cc_final: 0.9210 (p) REVERT: G 297 LEU cc_start: 0.9103 (tp) cc_final: 0.8856 (tp) REVERT: J 18 LEU cc_start: 0.8810 (tp) cc_final: 0.8497 (tp) REVERT: J 88 MET cc_start: 0.8511 (mmm) cc_final: 0.8242 (mmm) REVERT: J 187 TYR cc_start: 0.8872 (t80) cc_final: 0.8467 (t80) REVERT: J 202 ASP cc_start: 0.8398 (p0) cc_final: 0.7820 (t0) REVERT: J 311 ASP cc_start: 0.9258 (p0) cc_final: 0.8909 (p0) REVERT: K 36 ASN cc_start: 0.8852 (t0) cc_final: 0.7646 (t0) REVERT: K 57 ASN cc_start: 0.9213 (p0) cc_final: 0.8936 (p0) REVERT: K 70 MET cc_start: 0.8218 (tpt) cc_final: 0.7556 (tpt) REVERT: K 144 LEU cc_start: 0.8613 (tp) cc_final: 0.8112 (tp) REVERT: K 157 VAL cc_start: 0.9328 (t) cc_final: 0.8986 (p) REVERT: K 241 PHE cc_start: 0.9088 (t80) cc_final: 0.8738 (t80) REVERT: K 245 ASP cc_start: 0.9166 (m-30) cc_final: 0.8811 (m-30) REVERT: K 297 LEU cc_start: 0.9062 (tp) cc_final: 0.8767 (tp) REVERT: K 322 PHE cc_start: 0.9105 (m-80) cc_final: 0.8791 (m-80) REVERT: S 36 TRP cc_start: 0.6817 (m100) cc_final: 0.6022 (m100) REVERT: S 59 THR cc_start: 0.8669 (p) cc_final: 0.8375 (t) REVERT: S 77 LYS cc_start: 0.8920 (pttm) cc_final: 0.8474 (pttm) REVERT: S 80 LEU cc_start: 0.8875 (tp) cc_final: 0.8411 (tp) REVERT: S 101 VAL cc_start: 0.8920 (p) cc_final: 0.8613 (m) REVERT: S 103 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7203 (tm-30) REVERT: T 19 ARG cc_start: 0.8000 (mtm-85) cc_final: 0.7348 (mmt-90) REVERT: T 26 ASN cc_start: 0.8774 (t0) cc_final: 0.8177 (t0) REVERT: T 73 THR cc_start: 0.9194 (m) cc_final: 0.8939 (m) REVERT: T 106 LEU cc_start: 0.8562 (mm) cc_final: 0.8040 (mm) REVERT: U 29 PHE cc_start: 0.8379 (t80) cc_final: 0.8095 (t80) REVERT: U 32 TYR cc_start: 0.8498 (m-80) cc_final: 0.8285 (m-10) REVERT: U 33 ARG cc_start: 0.8669 (ttm110) cc_final: 0.8224 (ttp-110) REVERT: U 80 LEU cc_start: 0.9193 (tp) cc_final: 0.8891 (tp) REVERT: U 100 VAL cc_start: 0.7780 (t) cc_final: 0.7577 (t) REVERT: U 102 THR cc_start: 0.8380 (m) cc_final: 0.8118 (m) REVERT: V 31 LEU cc_start: 0.7970 (mm) cc_final: 0.7759 (mm) REVERT: V 95 ASP cc_start: 0.6837 (t0) cc_final: 0.6423 (t0) outliers start: 3 outliers final: 1 residues processed: 428 average time/residue: 0.1418 time to fit residues: 94.2070 Evaluate side-chains 301 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 300 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 249 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 HIS A 345 HIS ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN B 275 HIS ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 HIS ** G 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 275 HIS G 289 HIS ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 230 HIS J 270 ASN J 345 HIS K 99 HIS K 107 GLN K 289 HIS S 39 GLN T 41 GLN U 85 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.077947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.059625 restraints weight = 90212.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.061441 restraints weight = 47879.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.062681 restraints weight = 30710.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.063486 restraints weight = 22363.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.064011 restraints weight = 17971.496| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 20897 Z= 0.291 Angle : 0.753 10.575 28484 Z= 0.397 Chirality : 0.048 0.264 3161 Planarity : 0.005 0.053 3657 Dihedral : 6.125 29.952 2856 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.53 % Favored : 93.43 % Rotamer: Outliers : 0.18 % Allowed : 4.60 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.10 % 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: -1.23 (0.16), residues: 2618 helix: -0.90 (0.71), residues: 45 sheet: -0.74 (0.15), residues: 1110 loop : -0.78 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 135 TYR 0.028 0.002 TYR T 48 PHE 0.028 0.002 PHE K 145 TRP 0.025 0.002 TRP G 282 HIS 0.009 0.002 HIS K 275 Details of bonding type rmsd covalent geometry : bond 0.00631 (20854) covalent geometry : angle 0.74385 (28398) SS BOND : bond 0.00508 ( 43) SS BOND : angle 2.24611 ( 86) hydrogen bonds : bond 0.03811 ( 666) hydrogen bonds : angle 6.17897 ( 1797) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 381 time to evaluate : 0.866 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: A 29 LEU cc_start: 0.8928 (mt) cc_final: 0.8586 (mt) REVERT: A 251 LEU cc_start: 0.9574 (mt) cc_final: 0.9204 (mp) REVERT: B 40 GLU cc_start: 0.8763 (mp0) cc_final: 0.8430 (mm-30) REVERT: B 42 ASP cc_start: 0.8233 (m-30) cc_final: 0.8002 (m-30) REVERT: B 49 GLN cc_start: 0.8657 (tt0) cc_final: 0.8276 (tt0) REVERT: B 297 LEU cc_start: 0.9646 (tp) cc_final: 0.9187 (tp) REVERT: F 99 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7603 (tm-30) REVERT: F 195 MET cc_start: 0.8685 (mpp) cc_final: 0.8121 (mpp) REVERT: F 196 LYS cc_start: 0.9220 (mmmt) cc_final: 0.9018 (mmmt) REVERT: F 216 ARG cc_start: 0.8188 (mtp-110) cc_final: 0.7603 (mtp-110) REVERT: G 70 MET cc_start: 0.8407 (tpt) cc_final: 0.7960 (tpt) REVERT: G 141 GLU cc_start: 0.8878 (pm20) cc_final: 0.8600 (pm20) REVERT: G 241 PHE cc_start: 0.9321 (t80) cc_final: 0.9015 (t80) REVERT: G 282 TRP cc_start: 0.8723 (p-90) cc_final: 0.8254 (p-90) REVERT: G 291 THR cc_start: 0.9395 (m) cc_final: 0.9186 (p) REVERT: G 297 LEU cc_start: 0.9371 (tp) cc_final: 0.9082 (tp) REVERT: J 187 TYR cc_start: 0.8994 (t80) cc_final: 0.8585 (t80) REVERT: J 202 ASP cc_start: 0.8309 (p0) cc_final: 0.7615 (t0) REVERT: J 311 ASP cc_start: 0.9296 (p0) cc_final: 0.8979 (p0) REVERT: K 36 ASN cc_start: 0.8896 (t0) cc_final: 0.7562 (t0) REVERT: K 49 GLN cc_start: 0.9370 (pt0) cc_final: 0.9134 (pt0) REVERT: K 57 ASN cc_start: 0.9396 (p0) cc_final: 0.9100 (p0) REVERT: K 70 MET cc_start: 0.8694 (tpt) cc_final: 0.8491 (tpt) REVERT: K 105 LEU cc_start: 0.9279 (tt) cc_final: 0.8931 (tt) REVERT: K 144 LEU cc_start: 0.8658 (tp) cc_final: 0.8065 (tp) REVERT: K 145 PHE cc_start: 0.8764 (m-10) cc_final: 0.8424 (m-10) REVERT: K 245 ASP cc_start: 0.9085 (m-30) cc_final: 0.8785 (m-30) REVERT: K 297 LEU cc_start: 0.9199 (tp) cc_final: 0.8909 (tp) REVERT: S 34 MET cc_start: 0.8278 (mmt) cc_final: 0.7046 (mpp) REVERT: S 59 THR cc_start: 0.8740 (p) cc_final: 0.8437 (t) REVERT: S 74 ASP cc_start: 0.9339 (t0) cc_final: 0.8888 (p0) REVERT: S 82 LEU cc_start: 0.8317 (tp) cc_final: 0.7744 (tp) REVERT: S 101 VAL cc_start: 0.9135 (p) cc_final: 0.8858 (m) REVERT: S 103 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7449 (tm-30) REVERT: T 4 LEU cc_start: 0.7713 (mp) cc_final: 0.7391 (mt) REVERT: T 19 ARG cc_start: 0.8072 (mtm-85) cc_final: 0.7487 (mmt-90) REVERT: T 26 ASN cc_start: 0.9005 (t0) cc_final: 0.8347 (t0) REVERT: T 106 LEU cc_start: 0.8672 (mm) cc_final: 0.8436 (mm) REVERT: U 29 PHE cc_start: 0.8580 (t80) cc_final: 0.8072 (t80) REVERT: U 33 ARG cc_start: 0.8686 (ttm110) cc_final: 0.8232 (ttp-110) REVERT: U 80 LEU cc_start: 0.9042 (tp) cc_final: 0.8722 (tp) REVERT: U 103 GLU cc_start: 0.7203 (mp0) cc_final: 0.6981 (mp0) outliers start: 4 outliers final: 2 residues processed: 384 average time/residue: 0.1511 time to fit residues: 89.6144 Evaluate side-chains 262 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 260 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 214 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 238 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 chunk 71 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 GLN J 270 ASN K 107 GLN K 177 HIS ** K 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 289 HIS T 36 GLN U 85 HIS ** V 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.079681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.061479 restraints weight = 89369.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.063373 restraints weight = 46624.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.064633 restraints weight = 29698.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.065469 restraints weight = 21461.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.066011 restraints weight = 17149.521| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20897 Z= 0.164 Angle : 0.673 9.183 28484 Z= 0.351 Chirality : 0.047 0.166 3161 Planarity : 0.004 0.043 3657 Dihedral : 5.866 29.410 2856 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.04 % Allowed : 2.99 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.10 % 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: -1.18 (0.16), residues: 2618 helix: -0.78 (0.72), residues: 45 sheet: -0.77 (0.15), residues: 1149 loop : -0.68 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 134 TYR 0.020 0.001 TYR T 48 PHE 0.023 0.002 PHE G 262 TRP 0.022 0.002 TRP U 36 HIS 0.006 0.001 HIS V 96 Details of bonding type rmsd covalent geometry : bond 0.00375 (20854) covalent geometry : angle 0.66058 (28398) SS BOND : bond 0.00411 ( 43) SS BOND : angle 2.39921 ( 86) hydrogen bonds : bond 0.03230 ( 666) hydrogen bonds : angle 5.83866 ( 1797) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 394 time to evaluate : 0.852 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: A 15 TYR cc_start: 0.8180 (t80) cc_final: 0.7791 (t80) REVERT: A 79 ARG cc_start: 0.8549 (ptm-80) cc_final: 0.8201 (ptm-80) REVERT: A 246 ASN cc_start: 0.9278 (m-40) cc_final: 0.8922 (m-40) REVERT: A 251 LEU cc_start: 0.9568 (mt) cc_final: 0.9269 (mp) REVERT: B 40 GLU cc_start: 0.8776 (mp0) cc_final: 0.8401 (mm-30) REVERT: B 42 ASP cc_start: 0.8317 (m-30) cc_final: 0.8107 (m-30) REVERT: B 49 GLN cc_start: 0.8866 (tt0) cc_final: 0.8345 (tt0) REVERT: B 180 LYS cc_start: 0.8971 (ptmm) cc_final: 0.8635 (tptt) REVERT: B 297 LEU cc_start: 0.9534 (tp) cc_final: 0.9166 (tp) REVERT: F 99 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7578 (tm-30) REVERT: F 103 LEU cc_start: 0.9205 (mt) cc_final: 0.8247 (mt) REVERT: F 187 TYR cc_start: 0.9343 (t80) cc_final: 0.9139 (t80) REVERT: F 232 PRO cc_start: 0.8886 (Cg_exo) cc_final: 0.8271 (Cg_endo) REVERT: G 21 TYR cc_start: 0.7691 (m-10) cc_final: 0.7415 (m-80) REVERT: G 70 MET cc_start: 0.8349 (tpt) cc_final: 0.8087 (tpt) REVERT: G 241 PHE cc_start: 0.9350 (t80) cc_final: 0.9100 (t80) REVERT: G 282 TRP cc_start: 0.8691 (p-90) cc_final: 0.8383 (p-90) REVERT: G 291 THR cc_start: 0.9343 (m) cc_final: 0.9093 (p) REVERT: G 297 LEU cc_start: 0.9304 (tp) cc_final: 0.9016 (tp) REVERT: J 187 TYR cc_start: 0.8895 (t80) cc_final: 0.8459 (t80) REVERT: J 202 ASP cc_start: 0.8318 (p0) cc_final: 0.7685 (t0) REVERT: J 253 GLU cc_start: 0.9053 (pm20) cc_final: 0.8808 (pm20) REVERT: J 311 ASP cc_start: 0.9303 (p0) cc_final: 0.9009 (p0) REVERT: J 385 ASP cc_start: 0.9184 (t0) cc_final: 0.8944 (t70) REVERT: J 387 ILE cc_start: 0.7824 (tp) cc_final: 0.7266 (tp) REVERT: K 36 ASN cc_start: 0.8873 (t0) cc_final: 0.8664 (m-40) REVERT: K 49 GLN cc_start: 0.9277 (pt0) cc_final: 0.8854 (pt0) REVERT: K 57 ASN cc_start: 0.9422 (p0) cc_final: 0.9132 (p0) REVERT: K 144 LEU cc_start: 0.8623 (tp) cc_final: 0.8091 (tp) REVERT: K 241 PHE cc_start: 0.9158 (t80) cc_final: 0.8688 (t80) REVERT: K 245 ASP cc_start: 0.9035 (m-30) cc_final: 0.8756 (m-30) REVERT: K 297 LEU cc_start: 0.9192 (tp) cc_final: 0.8861 (tp) REVERT: K 322 PHE cc_start: 0.8918 (m-80) cc_final: 0.8646 (m-80) REVERT: S 34 MET cc_start: 0.8011 (mmt) cc_final: 0.6848 (mpp) REVERT: S 59 THR cc_start: 0.8773 (p) cc_final: 0.8458 (t) REVERT: S 74 ASP cc_start: 0.9380 (t0) cc_final: 0.9002 (p0) REVERT: S 82 LEU cc_start: 0.8179 (tp) cc_final: 0.7674 (tp) REVERT: S 101 VAL cc_start: 0.9057 (p) cc_final: 0.8840 (m) REVERT: S 103 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7715 (tm-30) REVERT: T 36 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8430 (pp30) REVERT: T 72 LEU cc_start: 0.9103 (tp) cc_final: 0.8763 (tp) REVERT: T 106 LEU cc_start: 0.8784 (mm) cc_final: 0.8327 (mm) REVERT: U 27 PHE cc_start: 0.8895 (p90) cc_final: 0.8387 (p90) REVERT: U 28 THR cc_start: 0.9106 (p) cc_final: 0.8701 (p) REVERT: U 29 PHE cc_start: 0.8595 (t80) cc_final: 0.8362 (t80) REVERT: U 33 ARG cc_start: 0.8689 (ttm110) cc_final: 0.8260 (ttp-110) REVERT: U 36 TRP cc_start: 0.5732 (m100) cc_final: 0.5365 (m100) REVERT: U 69 PHE cc_start: 0.8587 (m-80) cc_final: 0.7465 (m-80) REVERT: U 80 LEU cc_start: 0.9190 (tp) cc_final: 0.8717 (tp) REVERT: U 81 TYR cc_start: 0.8621 (m-80) cc_final: 0.8317 (m-10) REVERT: U 100 VAL cc_start: 0.8292 (t) cc_final: 0.7701 (t) outliers start: 1 outliers final: 0 residues processed: 394 average time/residue: 0.1443 time to fit residues: 88.7883 Evaluate side-chains 286 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 248 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 HIS B 53 GLN ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 235 GLN ** G 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 270 ASN K 107 GLN ** K 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 289 HIS ** T 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 HIS ** V 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.077596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.059143 restraints weight = 89381.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.060980 restraints weight = 47533.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.062216 restraints weight = 30634.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.063032 restraints weight = 22327.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.063583 restraints weight = 17939.059| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 20897 Z= 0.231 Angle : 0.704 10.906 28484 Z= 0.370 Chirality : 0.047 0.238 3161 Planarity : 0.005 0.091 3657 Dihedral : 5.998 32.995 2856 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.49 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.14 (0.16), residues: 2618 helix: -0.77 (0.74), residues: 45 sheet: -0.71 (0.15), residues: 1140 loop : -0.70 (0.17), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 99 TYR 0.042 0.002 TYR G 21 PHE 0.023 0.002 PHE K 262 TRP 0.024 0.002 TRP K 333 HIS 0.013 0.002 HIS K 172 Details of bonding type rmsd covalent geometry : bond 0.00504 (20854) covalent geometry : angle 0.69128 (28398) SS BOND : bond 0.00560 ( 43) SS BOND : angle 2.53776 ( 86) hydrogen bonds : bond 0.03421 ( 666) hydrogen bonds : angle 5.85434 ( 1797) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 TYR cc_start: 0.8067 (t80) cc_final: 0.7491 (t80) REVERT: A 16 LYS cc_start: 0.9270 (mptt) cc_final: 0.8867 (tptp) REVERT: A 29 LEU cc_start: 0.8924 (mt) cc_final: 0.8510 (mt) REVERT: A 79 ARG cc_start: 0.8672 (ptm-80) cc_final: 0.8340 (ptm-80) REVERT: A 93 GLN cc_start: 0.8376 (mm-40) cc_final: 0.8153 (mp10) REVERT: A 246 ASN cc_start: 0.9247 (m-40) cc_final: 0.8935 (m-40) REVERT: B 40 GLU cc_start: 0.8825 (mp0) cc_final: 0.8523 (mm-30) REVERT: B 49 GLN cc_start: 0.8783 (tt0) cc_final: 0.8022 (tm-30) REVERT: B 241 PHE cc_start: 0.9200 (t80) cc_final: 0.8995 (t80) REVERT: B 297 LEU cc_start: 0.9580 (tp) cc_final: 0.9218 (tp) REVERT: F 10 VAL cc_start: 0.9441 (m) cc_final: 0.9151 (m) REVERT: F 99 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7727 (tm-30) REVERT: F 232 PRO cc_start: 0.8814 (Cg_exo) cc_final: 0.8024 (Cg_endo) REVERT: F 253 GLU cc_start: 0.9170 (pm20) cc_final: 0.8740 (pm20) REVERT: G 49 GLN cc_start: 0.8971 (tt0) cc_final: 0.8455 (tt0) REVERT: G 70 MET cc_start: 0.8540 (tpt) cc_final: 0.8109 (tpt) REVERT: G 282 TRP cc_start: 0.8870 (p-90) cc_final: 0.7696 (p-90) REVERT: G 291 THR cc_start: 0.9377 (m) cc_final: 0.9165 (p) REVERT: G 297 LEU cc_start: 0.9342 (tp) cc_final: 0.9113 (tp) REVERT: J 88 MET cc_start: 0.8559 (mmm) cc_final: 0.8300 (mmm) REVERT: J 109 GLU cc_start: 0.8975 (pp20) cc_final: 0.8603 (pp20) REVERT: J 187 TYR cc_start: 0.8915 (t80) cc_final: 0.8420 (t80) REVERT: J 195 MET cc_start: 0.8601 (mpp) cc_final: 0.8308 (mpp) REVERT: J 202 ASP cc_start: 0.8315 (p0) cc_final: 0.7714 (t0) REVERT: J 311 ASP cc_start: 0.9315 (p0) cc_final: 0.9029 (p0) REVERT: J 387 ILE cc_start: 0.7944 (tp) cc_final: 0.7460 (tp) REVERT: K 84 ASP cc_start: 0.8545 (t0) cc_final: 0.8330 (t0) REVERT: K 124 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7139 (tp30) REVERT: K 144 LEU cc_start: 0.8764 (tp) cc_final: 0.8009 (tp) REVERT: K 241 PHE cc_start: 0.9102 (t80) cc_final: 0.8579 (t80) REVERT: K 283 PHE cc_start: 0.7508 (m-80) cc_final: 0.6704 (m-10) REVERT: K 297 LEU cc_start: 0.9160 (tp) cc_final: 0.8893 (tp) REVERT: K 308 ASP cc_start: 0.8630 (m-30) cc_final: 0.8362 (m-30) REVERT: K 327 GLU cc_start: 0.8134 (pp20) cc_final: 0.7751 (pp20) REVERT: S 34 MET cc_start: 0.8066 (mmt) cc_final: 0.7048 (mpp) REVERT: S 59 THR cc_start: 0.8891 (p) cc_final: 0.8636 (t) REVERT: S 82 LEU cc_start: 0.8390 (tp) cc_final: 0.7973 (tp) REVERT: T 19 ARG cc_start: 0.8157 (mtm-85) cc_final: 0.7469 (mmt-90) REVERT: T 106 LEU cc_start: 0.8762 (mm) cc_final: 0.8486 (mm) REVERT: U 18 LEU cc_start: 0.9591 (mt) cc_final: 0.9367 (mt) REVERT: U 27 PHE cc_start: 0.8996 (p90) cc_final: 0.8608 (p90) REVERT: U 29 PHE cc_start: 0.8546 (t80) cc_final: 0.8025 (t80) REVERT: U 32 TYR cc_start: 0.8622 (m-80) cc_final: 0.8352 (m-80) REVERT: U 33 ARG cc_start: 0.8733 (ttm110) cc_final: 0.8238 (ttp-110) REVERT: U 36 TRP cc_start: 0.5645 (m100) cc_final: 0.5335 (m100) REVERT: U 46 GLU cc_start: 0.7008 (mp0) cc_final: 0.6796 (mp0) REVERT: U 69 PHE cc_start: 0.8755 (m-80) cc_final: 0.8466 (m-80) REVERT: U 80 LEU cc_start: 0.9282 (tp) cc_final: 0.8760 (tp) REVERT: U 81 TYR cc_start: 0.8821 (m-80) cc_final: 0.8498 (m-10) REVERT: U 82 LEU cc_start: 0.9344 (tp) cc_final: 0.8991 (tp) REVERT: U 100 VAL cc_start: 0.7764 (t) cc_final: 0.7245 (t) REVERT: U 102 THR cc_start: 0.8432 (m) cc_final: 0.8195 (m) REVERT: V 96 HIS cc_start: 0.8212 (m90) cc_final: 0.7932 (m-70) REVERT: V 105 ARG cc_start: 0.8419 (tpt90) cc_final: 0.8041 (tpt90) REVERT: V 106 LEU cc_start: 0.8584 (tp) cc_final: 0.8357 (tp) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.1495 time to fit residues: 85.2940 Evaluate side-chains 277 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 224 optimal weight: 6.9990 chunk 140 optimal weight: 0.2980 chunk 155 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 208 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 137 optimal weight: 0.4980 chunk 159 optimal weight: 0.2980 chunk 52 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 270 ASN K 36 ASN K 49 GLN K 107 GLN K 255 GLN K 289 HIS ** T 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 HIS ** V 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.079686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.061214 restraints weight = 88588.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.063117 restraints weight = 46483.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.064390 restraints weight = 29640.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.065244 restraints weight = 21495.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.065787 restraints weight = 17182.333| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20897 Z= 0.134 Angle : 0.673 8.896 28484 Z= 0.350 Chirality : 0.047 0.184 3161 Planarity : 0.004 0.046 3657 Dihedral : 5.780 32.679 2856 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.81 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.02 (0.16), residues: 2618 helix: -0.44 (0.78), residues: 45 sheet: -0.65 (0.14), residues: 1191 loop : -0.58 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 326 TYR 0.030 0.001 TYR G 21 PHE 0.023 0.002 PHE U 69 TRP 0.019 0.001 TRP K 333 HIS 0.010 0.001 HIS G 177 Details of bonding type rmsd covalent geometry : bond 0.00309 (20854) covalent geometry : angle 0.66051 (28398) SS BOND : bond 0.00390 ( 43) SS BOND : angle 2.41493 ( 86) hydrogen bonds : bond 0.03235 ( 666) hydrogen bonds : angle 5.61714 ( 1797) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 TYR cc_start: 0.7871 (t80) cc_final: 0.7582 (t80) REVERT: A 16 LYS cc_start: 0.9216 (mptt) cc_final: 0.8918 (mmtm) REVERT: A 29 LEU cc_start: 0.8890 (mt) cc_final: 0.8583 (mt) REVERT: A 79 ARG cc_start: 0.8619 (ptm-80) cc_final: 0.8338 (ptm-80) REVERT: A 195 MET cc_start: 0.8208 (mpp) cc_final: 0.7890 (mtt) REVERT: A 246 ASN cc_start: 0.9255 (m-40) cc_final: 0.8923 (m-40) REVERT: A 251 LEU cc_start: 0.9531 (mt) cc_final: 0.9288 (mp) REVERT: B 40 GLU cc_start: 0.8843 (mp0) cc_final: 0.8458 (mm-30) REVERT: B 49 GLN cc_start: 0.8855 (tt0) cc_final: 0.8271 (tt0) REVERT: B 297 LEU cc_start: 0.9538 (tp) cc_final: 0.9180 (tp) REVERT: F 99 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7705 (tm-30) REVERT: F 103 LEU cc_start: 0.9081 (mt) cc_final: 0.8774 (mt) REVERT: F 220 ARG cc_start: 0.8658 (ptp90) cc_final: 0.7988 (ptp90) REVERT: F 232 PRO cc_start: 0.8813 (Cg_exo) cc_final: 0.8021 (Cg_endo) REVERT: G 36 ASN cc_start: 0.9219 (t0) cc_final: 0.8903 (t0) REVERT: G 53 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7481 (mm-40) REVERT: G 112 ASP cc_start: 0.8410 (m-30) cc_final: 0.7837 (m-30) REVERT: G 177 HIS cc_start: 0.8041 (t-90) cc_final: 0.7351 (t-90) REVERT: G 282 TRP cc_start: 0.8754 (p-90) cc_final: 0.8217 (p-90) REVERT: G 291 THR cc_start: 0.9294 (m) cc_final: 0.9020 (p) REVERT: G 297 LEU cc_start: 0.9295 (tp) cc_final: 0.8887 (tp) REVERT: J 88 MET cc_start: 0.8378 (mmm) cc_final: 0.8138 (mmm) REVERT: J 109 GLU cc_start: 0.8869 (pp20) cc_final: 0.8232 (pp20) REVERT: J 187 TYR cc_start: 0.8873 (t80) cc_final: 0.8417 (t80) REVERT: J 202 ASP cc_start: 0.8291 (p0) cc_final: 0.7641 (t0) REVERT: J 311 ASP cc_start: 0.9309 (p0) cc_final: 0.9035 (p0) REVERT: K 84 ASP cc_start: 0.8543 (t0) cc_final: 0.8300 (t0) REVERT: K 144 LEU cc_start: 0.8719 (tp) cc_final: 0.7898 (tp) REVERT: K 171 MET cc_start: 0.8117 (pmm) cc_final: 0.7860 (pmm) REVERT: K 239 TRP cc_start: 0.7893 (m-10) cc_final: 0.7513 (m-90) REVERT: K 241 PHE cc_start: 0.8987 (t80) cc_final: 0.8482 (t80) REVERT: K 283 PHE cc_start: 0.7614 (m-80) cc_final: 0.6735 (m-10) REVERT: K 297 LEU cc_start: 0.9028 (tp) cc_final: 0.8663 (tp) REVERT: K 327 GLU cc_start: 0.8162 (pp20) cc_final: 0.7815 (pp20) REVERT: K 333 TRP cc_start: 0.8995 (t-100) cc_final: 0.8513 (t-100) REVERT: S 34 MET cc_start: 0.7962 (mmt) cc_final: 0.7021 (mpp) REVERT: S 59 THR cc_start: 0.8964 (p) cc_final: 0.8717 (t) REVERT: S 77 LYS cc_start: 0.9246 (pttm) cc_final: 0.8865 (pttp) REVERT: S 82 LEU cc_start: 0.8288 (tp) cc_final: 0.7990 (tp) REVERT: T 106 LEU cc_start: 0.8892 (mm) cc_final: 0.8385 (mm) REVERT: U 27 PHE cc_start: 0.8961 (p90) cc_final: 0.8404 (p90) REVERT: U 29 PHE cc_start: 0.8504 (t80) cc_final: 0.7960 (t80) REVERT: U 32 TYR cc_start: 0.8654 (m-80) cc_final: 0.8445 (m-10) REVERT: U 33 ARG cc_start: 0.8655 (ttm110) cc_final: 0.8227 (ttp-110) REVERT: U 36 TRP cc_start: 0.5632 (m100) cc_final: 0.5219 (m100) REVERT: U 46 GLU cc_start: 0.7063 (mp0) cc_final: 0.6832 (mp0) REVERT: U 69 PHE cc_start: 0.8830 (m-80) cc_final: 0.8601 (m-10) REVERT: U 80 LEU cc_start: 0.9206 (tp) cc_final: 0.8775 (tp) REVERT: U 81 TYR cc_start: 0.8867 (m-80) cc_final: 0.8567 (m-10) REVERT: U 100 VAL cc_start: 0.7984 (t) cc_final: 0.7417 (t) REVERT: V 47 ILE cc_start: 0.8962 (mm) cc_final: 0.8757 (mm) REVERT: V 57 ILE cc_start: 0.7707 (mp) cc_final: 0.7141 (mp) REVERT: V 95 ASP cc_start: 0.7268 (t0) cc_final: 0.6686 (t0) REVERT: V 105 ARG cc_start: 0.8333 (tpt90) cc_final: 0.7913 (tpt90) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.1540 time to fit residues: 92.2903 Evaluate side-chains 279 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 106 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 230 optimal weight: 0.0170 chunk 227 optimal weight: 0.9980 chunk 219 optimal weight: 2.9990 chunk 241 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 233 optimal weight: 0.0670 chunk 64 optimal weight: 0.0980 chunk 165 optimal weight: 0.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 HIS ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 GLN K 289 HIS T 41 GLN U 39 GLN U 85 HIS ** V 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.080839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.062517 restraints weight = 88118.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.064421 restraints weight = 46539.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.065687 restraints weight = 29786.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.066548 restraints weight = 21633.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.067066 restraints weight = 17276.200| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20897 Z= 0.123 Angle : 0.668 9.828 28484 Z= 0.346 Chirality : 0.047 0.187 3161 Planarity : 0.004 0.046 3657 Dihedral : 5.683 33.085 2856 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.04 % Allowed : 1.25 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.98 (0.16), residues: 2618 helix: -0.46 (0.79), residues: 45 sheet: -0.64 (0.14), residues: 1212 loop : -0.53 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 134 TYR 0.027 0.001 TYR K 209 PHE 0.041 0.002 PHE U 69 TRP 0.017 0.001 TRP K 282 HIS 0.010 0.001 HIS V 96 Details of bonding type rmsd covalent geometry : bond 0.00290 (20854) covalent geometry : angle 0.65402 (28398) SS BOND : bond 0.00382 ( 43) SS BOND : angle 2.53905 ( 86) hydrogen bonds : bond 0.03252 ( 666) hydrogen bonds : angle 5.51372 ( 1797) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 383 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.9177 (mptt) cc_final: 0.8884 (tptp) REVERT: A 29 LEU cc_start: 0.8855 (mt) cc_final: 0.8299 (mt) REVERT: A 79 ARG cc_start: 0.8664 (ptm-80) cc_final: 0.8375 (ptm-80) REVERT: A 195 MET cc_start: 0.8033 (mpp) cc_final: 0.6982 (mtm) REVERT: A 246 ASN cc_start: 0.9263 (m-40) cc_final: 0.8940 (m-40) REVERT: A 251 LEU cc_start: 0.9522 (mt) cc_final: 0.9275 (mp) REVERT: A 253 GLU cc_start: 0.8475 (pm20) cc_final: 0.8265 (pm20) REVERT: B 40 GLU cc_start: 0.8871 (mp0) cc_final: 0.8455 (mm-30) REVERT: B 246 LEU cc_start: 0.9263 (mt) cc_final: 0.9057 (pp) REVERT: B 297 LEU cc_start: 0.9538 (tp) cc_final: 0.9200 (tp) REVERT: F 31 ILE cc_start: 0.9342 (mp) cc_final: 0.9039 (mp) REVERT: F 99 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7705 (tm-30) REVERT: F 103 LEU cc_start: 0.9119 (mt) cc_final: 0.8779 (mt) REVERT: F 220 ARG cc_start: 0.8746 (ptp90) cc_final: 0.8046 (ptp90) REVERT: F 232 PRO cc_start: 0.8821 (Cg_exo) cc_final: 0.8429 (Cg_endo) REVERT: F 390 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8353 (tm-30) REVERT: G 36 ASN cc_start: 0.9212 (t0) cc_final: 0.8888 (t0) REVERT: G 49 GLN cc_start: 0.8956 (tt0) cc_final: 0.8398 (tt0) REVERT: G 53 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7628 (mp10) REVERT: G 112 ASP cc_start: 0.8435 (m-30) cc_final: 0.7847 (m-30) REVERT: G 177 HIS cc_start: 0.8009 (t-90) cc_final: 0.7489 (t-90) REVERT: G 282 TRP cc_start: 0.8747 (p-90) cc_final: 0.8039 (p-90) REVERT: G 291 THR cc_start: 0.9240 (m) cc_final: 0.8965 (p) REVERT: G 297 LEU cc_start: 0.9266 (tp) cc_final: 0.8863 (tp) REVERT: J 18 LEU cc_start: 0.8773 (tp) cc_final: 0.8484 (tp) REVERT: J 88 MET cc_start: 0.8376 (mmm) cc_final: 0.8155 (mmm) REVERT: J 109 GLU cc_start: 0.8974 (pp20) cc_final: 0.8265 (pp20) REVERT: J 187 TYR cc_start: 0.8853 (t80) cc_final: 0.8275 (t80) REVERT: J 195 MET cc_start: 0.8499 (mpp) cc_final: 0.8283 (mpp) REVERT: J 202 ASP cc_start: 0.8321 (p0) cc_final: 0.7609 (t0) REVERT: J 253 GLU cc_start: 0.9245 (pm20) cc_final: 0.8959 (pm20) REVERT: J 311 ASP cc_start: 0.9338 (p0) cc_final: 0.9112 (p0) REVERT: K 84 ASP cc_start: 0.8602 (t0) cc_final: 0.8317 (t0) REVERT: K 144 LEU cc_start: 0.8722 (tp) cc_final: 0.7908 (tp) REVERT: K 239 TRP cc_start: 0.7897 (m-10) cc_final: 0.7502 (m-90) REVERT: K 241 PHE cc_start: 0.8950 (t80) cc_final: 0.8508 (t80) REVERT: K 297 LEU cc_start: 0.9087 (tp) cc_final: 0.8715 (tp) REVERT: K 322 PHE cc_start: 0.8923 (m-80) cc_final: 0.8564 (m-80) REVERT: K 327 GLU cc_start: 0.8203 (pp20) cc_final: 0.7737 (pp20) REVERT: K 333 TRP cc_start: 0.8973 (t-100) cc_final: 0.8525 (t-100) REVERT: S 32 TYR cc_start: 0.7992 (m-80) cc_final: 0.7472 (m-80) REVERT: S 34 MET cc_start: 0.7852 (mmt) cc_final: 0.6867 (mpp) REVERT: S 59 THR cc_start: 0.8955 (p) cc_final: 0.8716 (t) REVERT: S 82 LEU cc_start: 0.8167 (tp) cc_final: 0.7738 (tp) REVERT: T 3 GLU cc_start: 0.8054 (pm20) cc_final: 0.7746 (pm20) REVERT: T 19 ARG cc_start: 0.8112 (mtm-85) cc_final: 0.7644 (mmt-90) REVERT: T 26 ASN cc_start: 0.8879 (t0) cc_final: 0.8572 (p0) REVERT: T 48 TYR cc_start: 0.8765 (p90) cc_final: 0.8484 (p90) REVERT: T 105 ARG cc_start: 0.8790 (tpp-160) cc_final: 0.8018 (tpm170) REVERT: T 106 LEU cc_start: 0.8578 (mm) cc_final: 0.7691 (mm) REVERT: U 27 PHE cc_start: 0.8981 (p90) cc_final: 0.8444 (p90) REVERT: U 29 PHE cc_start: 0.8528 (t80) cc_final: 0.7969 (t80) REVERT: U 32 TYR cc_start: 0.8623 (m-80) cc_final: 0.8297 (m-10) REVERT: U 33 ARG cc_start: 0.8660 (ttm110) cc_final: 0.8312 (ttp-110) REVERT: U 46 GLU cc_start: 0.6996 (mp0) cc_final: 0.6765 (mp0) REVERT: U 69 PHE cc_start: 0.8964 (m-80) cc_final: 0.8314 (m-10) REVERT: U 80 LEU cc_start: 0.9265 (tp) cc_final: 0.8932 (tp) REVERT: U 100 VAL cc_start: 0.8207 (t) cc_final: 0.7758 (t) REVERT: V 95 ASP cc_start: 0.6950 (t0) cc_final: 0.6734 (t0) REVERT: V 105 ARG cc_start: 0.8196 (tpt90) cc_final: 0.7745 (tpt90) outliers start: 1 outliers final: 0 residues processed: 384 average time/residue: 0.1509 time to fit residues: 88.8969 Evaluate side-chains 279 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 149 optimal weight: 0.4980 chunk 245 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 HIS ** G 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 270 ASN K 107 GLN K 289 HIS ** T 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.078309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.059989 restraints weight = 90050.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.061839 restraints weight = 48064.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.063074 restraints weight = 30933.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.063907 restraints weight = 22562.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.064422 restraints weight = 18089.434| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20897 Z= 0.200 Angle : 0.703 11.407 28484 Z= 0.366 Chirality : 0.047 0.265 3161 Planarity : 0.005 0.060 3657 Dihedral : 5.851 33.832 2856 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.53 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.99 (0.16), residues: 2618 helix: -0.43 (0.81), residues: 45 sheet: -0.67 (0.14), residues: 1212 loop : -0.53 (0.18), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 134 TYR 0.028 0.002 TYR G 21 PHE 0.034 0.002 PHE U 69 TRP 0.027 0.002 TRP G 282 HIS 0.012 0.001 HIS K 172 Details of bonding type rmsd covalent geometry : bond 0.00446 (20854) covalent geometry : angle 0.68479 (28398) SS BOND : bond 0.00699 ( 43) SS BOND : angle 2.96198 ( 86) hydrogen bonds : bond 0.03438 ( 666) hydrogen bonds : angle 5.65738 ( 1797) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.807 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 16 LYS cc_start: 0.9224 (mptt) cc_final: 0.8965 (tptp) REVERT: A 79 ARG cc_start: 0.8700 (ptm-80) cc_final: 0.8411 (ptm-80) REVERT: A 174 ASP cc_start: 0.9051 (m-30) cc_final: 0.8726 (t70) REVERT: A 246 ASN cc_start: 0.9252 (m-40) cc_final: 0.8951 (m-40) REVERT: B 40 GLU cc_start: 0.8856 (mp0) cc_final: 0.8500 (mm-30) REVERT: B 105 LEU cc_start: 0.9328 (tt) cc_final: 0.9127 (tt) REVERT: B 180 LYS cc_start: 0.9167 (tttp) cc_final: 0.8770 (tptt) REVERT: B 297 LEU cc_start: 0.9585 (tp) cc_final: 0.9227 (tp) REVERT: F 31 ILE cc_start: 0.9368 (mp) cc_final: 0.8967 (tp) REVERT: F 99 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7745 (tm-30) REVERT: F 103 LEU cc_start: 0.9168 (mt) cc_final: 0.8796 (mt) REVERT: F 218 ASP cc_start: 0.8787 (t0) cc_final: 0.8395 (t70) REVERT: F 232 PRO cc_start: 0.8737 (Cg_exo) cc_final: 0.7957 (Cg_endo) REVERT: F 373 LYS cc_start: 0.8997 (ttmt) cc_final: 0.8682 (ttmm) REVERT: F 390 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8446 (tm-30) REVERT: G 36 ASN cc_start: 0.9275 (t0) cc_final: 0.8960 (t0) REVERT: G 49 GLN cc_start: 0.9065 (tt0) cc_final: 0.8493 (tt0) REVERT: G 53 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7507 (mp10) REVERT: G 54 PHE cc_start: 0.8689 (m-80) cc_final: 0.8441 (m-80) REVERT: G 112 ASP cc_start: 0.8485 (m-30) cc_final: 0.7926 (m-30) REVERT: G 177 HIS cc_start: 0.8177 (t-90) cc_final: 0.7464 (t-90) REVERT: G 297 LEU cc_start: 0.9333 (tp) cc_final: 0.8903 (tp) REVERT: J 18 LEU cc_start: 0.8847 (tp) cc_final: 0.8632 (tp) REVERT: J 88 MET cc_start: 0.8625 (mmm) cc_final: 0.8412 (mmm) REVERT: J 109 GLU cc_start: 0.8952 (pp20) cc_final: 0.8148 (pp20) REVERT: J 195 MET cc_start: 0.8568 (mpp) cc_final: 0.8243 (mpp) REVERT: J 217 THR cc_start: 0.8015 (p) cc_final: 0.7602 (p) REVERT: J 253 GLU cc_start: 0.9267 (pm20) cc_final: 0.8918 (pm20) REVERT: J 311 ASP cc_start: 0.9321 (p0) cc_final: 0.9106 (p0) REVERT: K 70 MET cc_start: 0.8965 (tpt) cc_final: 0.8719 (tpt) REVERT: K 144 LEU cc_start: 0.8648 (tp) cc_final: 0.8099 (tp) REVERT: K 171 MET cc_start: 0.8092 (pmm) cc_final: 0.7837 (pmm) REVERT: K 239 TRP cc_start: 0.7896 (m-10) cc_final: 0.7540 (m-90) REVERT: K 241 PHE cc_start: 0.8992 (t80) cc_final: 0.8560 (t80) REVERT: K 283 PHE cc_start: 0.7935 (m-80) cc_final: 0.7154 (m-10) REVERT: K 297 LEU cc_start: 0.9123 (tp) cc_final: 0.8805 (tp) REVERT: K 327 GLU cc_start: 0.8265 (pp20) cc_final: 0.7890 (pp20) REVERT: S 20 LEU cc_start: 0.9175 (mp) cc_final: 0.8694 (mt) REVERT: S 34 MET cc_start: 0.7788 (mmt) cc_final: 0.7456 (mmt) REVERT: S 59 THR cc_start: 0.8917 (p) cc_final: 0.8647 (t) REVERT: S 82 LEU cc_start: 0.8353 (tp) cc_final: 0.7810 (tp) REVERT: T 105 ARG cc_start: 0.8847 (tpp-160) cc_final: 0.7988 (tpm170) REVERT: T 106 LEU cc_start: 0.8681 (mm) cc_final: 0.7776 (mm) REVERT: U 27 PHE cc_start: 0.8950 (p90) cc_final: 0.8346 (p90) REVERT: U 29 PHE cc_start: 0.8439 (t80) cc_final: 0.7869 (t80) REVERT: U 33 ARG cc_start: 0.8672 (ttm110) cc_final: 0.8213 (ttp-110) REVERT: U 46 GLU cc_start: 0.6952 (mp0) cc_final: 0.6701 (mp0) REVERT: U 69 PHE cc_start: 0.8894 (m-80) cc_final: 0.7955 (m-80) REVERT: U 80 LEU cc_start: 0.9326 (tp) cc_final: 0.9122 (tp) REVERT: U 81 TYR cc_start: 0.8959 (m-80) cc_final: 0.8698 (m-10) REVERT: U 100 VAL cc_start: 0.7954 (t) cc_final: 0.7549 (t) REVERT: U 103 GLU cc_start: 0.7224 (mp0) cc_final: 0.6853 (mp0) REVERT: V 95 ASP cc_start: 0.7260 (t0) cc_final: 0.6980 (t0) REVERT: V 105 ARG cc_start: 0.8202 (tpt90) cc_final: 0.7752 (tpt90) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.1467 time to fit residues: 80.7869 Evaluate side-chains 274 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 38 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 172 optimal weight: 0.0970 chunk 144 optimal weight: 4.9990 chunk 198 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 GLN K 177 HIS K 289 HIS ** T 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.077385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.059032 restraints weight = 90265.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.060846 restraints weight = 47940.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.062074 restraints weight = 30972.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.062883 restraints weight = 22592.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.063407 restraints weight = 18140.319| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20897 Z= 0.213 Angle : 0.730 10.201 28484 Z= 0.379 Chirality : 0.047 0.236 3161 Planarity : 0.005 0.119 3657 Dihedral : 5.992 34.245 2856 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.88 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.07 (0.16), residues: 2618 helix: -0.52 (0.79), residues: 45 sheet: -0.61 (0.15), residues: 1101 loop : -0.71 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG U 68 TYR 0.030 0.002 TYR G 21 PHE 0.033 0.002 PHE U 69 TRP 0.029 0.002 TRP G 282 HIS 0.011 0.001 HIS K 172 Details of bonding type rmsd covalent geometry : bond 0.00473 (20854) covalent geometry : angle 0.71515 (28398) SS BOND : bond 0.00473 ( 43) SS BOND : angle 2.76698 ( 86) hydrogen bonds : bond 0.03442 ( 666) hydrogen bonds : angle 5.67176 ( 1797) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.9249 (mptt) cc_final: 0.9045 (tptp) REVERT: A 79 ARG cc_start: 0.8672 (ptm-80) cc_final: 0.8369 (ptm-80) REVERT: A 174 ASP cc_start: 0.9032 (m-30) cc_final: 0.8811 (t70) REVERT: A 246 ASN cc_start: 0.9253 (m-40) cc_final: 0.8957 (m-40) REVERT: B 40 GLU cc_start: 0.8843 (mp0) cc_final: 0.8494 (mm-30) REVERT: B 177 HIS cc_start: 0.7665 (t70) cc_final: 0.7459 (t70) REVERT: B 297 LEU cc_start: 0.9585 (tp) cc_final: 0.9223 (tp) REVERT: F 31 ILE cc_start: 0.9351 (mp) cc_final: 0.8966 (tp) REVERT: F 99 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7772 (tm-30) REVERT: F 103 LEU cc_start: 0.9129 (mt) cc_final: 0.8751 (mt) REVERT: F 232 PRO cc_start: 0.8757 (Cg_exo) cc_final: 0.8505 (Cg_endo) REVERT: F 390 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8424 (tm-30) REVERT: G 32 ILE cc_start: 0.9367 (pt) cc_final: 0.9138 (pt) REVERT: G 36 ASN cc_start: 0.9199 (t0) cc_final: 0.8716 (t0) REVERT: G 48 ILE cc_start: 0.9590 (mm) cc_final: 0.9363 (mm) REVERT: G 49 GLN cc_start: 0.9127 (tt0) cc_final: 0.8791 (tt0) REVERT: G 53 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7552 (mp10) REVERT: G 177 HIS cc_start: 0.8226 (t-90) cc_final: 0.7504 (t-90) REVERT: G 297 LEU cc_start: 0.9322 (tp) cc_final: 0.8899 (tp) REVERT: J 88 MET cc_start: 0.8708 (mmm) cc_final: 0.8495 (mmm) REVERT: J 195 MET cc_start: 0.8560 (mpp) cc_final: 0.8304 (mpp) REVERT: J 202 ASP cc_start: 0.8232 (p0) cc_final: 0.7784 (t0) REVERT: J 253 GLU cc_start: 0.9257 (pm20) cc_final: 0.8922 (pm20) REVERT: J 311 ASP cc_start: 0.9320 (p0) cc_final: 0.9108 (p0) REVERT: K 49 GLN cc_start: 0.9191 (pt0) cc_final: 0.8926 (pt0) REVERT: K 70 MET cc_start: 0.8956 (tpt) cc_final: 0.8680 (tpt) REVERT: K 171 MET cc_start: 0.8250 (pmm) cc_final: 0.7711 (pmm) REVERT: K 239 TRP cc_start: 0.7871 (m-10) cc_final: 0.7549 (m-90) REVERT: K 241 PHE cc_start: 0.8999 (t80) cc_final: 0.8486 (t80) REVERT: K 283 PHE cc_start: 0.7981 (m-80) cc_final: 0.7172 (m-10) REVERT: K 297 LEU cc_start: 0.9082 (tp) cc_final: 0.8800 (tp) REVERT: K 344 GLN cc_start: 0.3405 (pp30) cc_final: 0.2988 (tm-30) REVERT: S 34 MET cc_start: 0.7814 (mmt) cc_final: 0.6862 (mpp) REVERT: S 84 MET cc_start: 0.9301 (mpp) cc_final: 0.9088 (mpp) REVERT: T 48 TYR cc_start: 0.8848 (p90) cc_final: 0.8546 (p90) REVERT: T 105 ARG cc_start: 0.8849 (tpp-160) cc_final: 0.7985 (tpm170) REVERT: T 106 LEU cc_start: 0.8791 (mm) cc_final: 0.7875 (mm) REVERT: U 27 PHE cc_start: 0.8866 (p90) cc_final: 0.7798 (p90) REVERT: U 28 THR cc_start: 0.9210 (p) cc_final: 0.8449 (p) REVERT: U 29 PHE cc_start: 0.8375 (t80) cc_final: 0.8120 (t80) REVERT: U 32 TYR cc_start: 0.8780 (m-10) cc_final: 0.8487 (m-10) REVERT: U 33 ARG cc_start: 0.8658 (ttm110) cc_final: 0.8222 (ttp-110) REVERT: U 46 GLU cc_start: 0.6943 (mp0) cc_final: 0.6704 (mp0) REVERT: U 69 PHE cc_start: 0.8960 (m-80) cc_final: 0.8459 (m-80) REVERT: U 80 LEU cc_start: 0.9408 (tp) cc_final: 0.9158 (tp) REVERT: U 81 TYR cc_start: 0.9010 (m-80) cc_final: 0.8721 (m-10) REVERT: V 95 ASP cc_start: 0.7613 (t0) cc_final: 0.7201 (t0) REVERT: V 105 ARG cc_start: 0.8233 (tpt90) cc_final: 0.7792 (tpt90) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.1482 time to fit residues: 80.3818 Evaluate side-chains 269 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 35 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 184 optimal weight: 0.3980 chunk 226 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 230 optimal weight: 0.5980 chunk 183 optimal weight: 0.8980 chunk 213 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS A 364 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 HIS ** G 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 235 GLN K 107 GLN K 177 HIS K 289 HIS ** T 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 HIS ** V 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.078836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.060372 restraints weight = 88753.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.062280 restraints weight = 47219.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.063538 restraints weight = 30129.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.064378 restraints weight = 21896.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.064923 restraints weight = 17479.805| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20897 Z= 0.145 Angle : 0.693 8.237 28484 Z= 0.358 Chirality : 0.047 0.243 3161 Planarity : 0.005 0.073 3657 Dihedral : 5.830 34.559 2856 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.11 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.97 (0.16), residues: 2618 helix: -0.32 (0.82), residues: 45 sheet: -0.55 (0.15), residues: 1098 loop : -0.64 (0.17), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 134 TYR 0.028 0.002 TYR G 21 PHE 0.037 0.002 PHE U 69 TRP 0.040 0.002 TRP U 36 HIS 0.017 0.001 HIS F 230 Details of bonding type rmsd covalent geometry : bond 0.00336 (20854) covalent geometry : angle 0.68107 (28398) SS BOND : bond 0.00402 ( 43) SS BOND : angle 2.42925 ( 86) hydrogen bonds : bond 0.03302 ( 666) hydrogen bonds : angle 5.55705 ( 1797) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4576.31 seconds wall clock time: 80 minutes 10.67 seconds (4810.67 seconds total)