Starting phenix.real_space_refine on Sat Jul 4 02:29:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d21_27139/07_2026/8d21_27139.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d21_27139/07_2026/8d21_27139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8d21_27139/07_2026/8d21_27139.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d21_27139/07_2026/8d21_27139.cif" model { file = "/net/cci-nas-00/data/ceres_data/8d21_27139/07_2026/8d21_27139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d21_27139/07_2026/8d21_27139.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d21_27139/07_2026/8d21_27139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d21_27139/07_2026/8d21_27139.map" } resolution = 3.96 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= 0.014 sd= 0.086 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 78 5.16 5 C 11019 2.51 5 N 2991 2.21 5 O 3453 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17541 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1396 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "A" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2536 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "H" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 950 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "C" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1396 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "D" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2536 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "E" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 950 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "F" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "G" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1396 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "I" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2536 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "J" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 950 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "K" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "I" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 4.03, per 1000 atoms: 0.23 Number of scatterers: 17541 At special positions: 0 Unit cell: (136.395, 132.065, 162.375, 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 78 16.00 O 3453 8.00 N 2991 7.00 C 11019 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS I 30 " distance=2.04 Simple disulfide: pdb=" SG CYS B 137 " - pdb=" SG CYS A 14 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS C 47 " distance=2.04 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS D 14 " distance=2.03 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS C 148 " distance=2.03 Simple disulfide: pdb=" SG CYS D 30 " - pdb=" SG CYS G 47 " distance=2.04 Simple disulfide: pdb=" SG CYS D 52 " - pdb=" SG CYS D 277 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 76 " distance=2.03 Simple disulfide: pdb=" SG CYS D 97 " - pdb=" SG CYS D 139 " distance=2.03 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 305 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 137 " - pdb=" SG CYS I 14 " distance=2.03 Simple disulfide: pdb=" SG CYS G 144 " - pdb=" SG CYS G 148 " distance=2.03 Simple disulfide: pdb=" SG CYS I 52 " - pdb=" SG CYS I 277 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 76 " distance=2.03 Simple disulfide: pdb=" SG CYS I 97 " - pdb=" SG CYS I 139 " distance=2.03 Simple disulfide: pdb=" SG CYS I 281 " - pdb=" SG CYS I 305 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 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 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 401 " - " ASN A 21 " " NAG A 402 " - " ASN A 129 " " NAG A 403 " - " ASN A 94 " " NAG A 404 " - " ASN A 33 " " NAG A 405 " - " ASN A 289 " " NAG A 406 " - " ASN A 63 " " NAG A 407 " - " ASN A 163 " " NAG D 401 " - " ASN D 21 " " NAG D 402 " - " ASN D 129 " " NAG D 403 " - " ASN D 94 " " NAG D 404 " - " ASN D 33 " " NAG D 405 " - " ASN D 289 " " NAG D 406 " - " ASN D 63 " " NAG D 407 " - " ASN D 163 " " NAG I 401 " - " ASN I 21 " " NAG I 402 " - " ASN I 129 " " NAG I 403 " - " ASN I 94 " " NAG I 404 " - " ASN I 33 " " NAG I 405 " - " ASN I 289 " " NAG I 406 " - " ASN I 63 " " NAG I 407 " - " ASN I 163 " " NAG M 1 " - " ASN B 154 " " NAG N 1 " - " ASN C 154 " " NAG O 1 " - " ASN G 154 " Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 750.5 milliseconds 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4002 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 51 sheets defined 19.5% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'B' and resid 1 through 7 removed outlier: 3.551A pdb=" N ILE B 6 " --> pdb=" O LEU B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 58 removed outlier: 3.814A pdb=" N GLN B 42 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N CYS B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 126 removed outlier: 3.784A pdb=" N GLU B 78 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 removed outlier: 3.777A pdb=" N SER B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL B 152 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS B 153 " --> pdb=" O MET B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 173 removed outlier: 3.565A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'H' and resid 52A through 55 removed outlier: 3.712A pdb=" N LEU H 55 " --> pdb=" O GLY H 52A" (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 52A through 55' Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 37 through 58 removed outlier: 3.859A pdb=" N GLN C 42 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN C 46 " --> pdb=" O GLN C 42 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N CYS C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 126 removed outlier: 3.777A pdb=" N GLU C 78 " --> pdb=" O GLU C 74 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 126 " --> pdb=" O VAL C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 154 removed outlier: 3.921A pdb=" N SER C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL C 152 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C 153 " --> pdb=" O MET C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 173 removed outlier: 3.598A pdb=" N TYR C 162 " --> pdb=" O ASP C 158 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU C 164 " --> pdb=" O PRO C 160 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLU C 165 " --> pdb=" O LYS C 161 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 71 Processing helix chain 'D' and resid 76 through 80 removed outlier: 3.923A pdb=" N LEU D 79 " --> pdb=" O CYS D 76 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE D 80 " --> pdb=" O GLU D 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 76 through 80' Processing helix chain 'D' and resid 104 through 112 Processing helix chain 'D' and resid 187 through 196 Processing helix chain 'E' and resid 52A through 55 removed outlier: 3.708A pdb=" N LEU E 55 " --> pdb=" O GLY E 52A" (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52A through 55' Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 37 through 58 removed outlier: 3.639A pdb=" N GLN G 42 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN G 43 " --> pdb=" O LYS G 39 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN G 46 " --> pdb=" O GLN G 42 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N CYS G 47 " --> pdb=" O ASN G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 73 No H-bonds generated for 'chain 'G' and resid 71 through 73' Processing helix chain 'G' and resid 74 through 126 removed outlier: 3.724A pdb=" N GLU G 78 " --> pdb=" O GLU G 74 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU G 105 " --> pdb=" O LEU G 101 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG G 106 " --> pdb=" O LEU G 102 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU G 126 " --> pdb=" O VAL G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 154 removed outlier: 3.747A pdb=" N SER G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL G 152 " --> pdb=" O CYS G 148 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS G 153 " --> pdb=" O MET G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 173 removed outlier: 3.646A pdb=" N TYR G 162 " --> pdb=" O ASP G 158 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU G 164 " --> pdb=" O PRO G 160 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU G 165 " --> pdb=" O LYS G 161 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU G 168 " --> pdb=" O GLU G 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 71 Processing helix chain 'I' and resid 104 through 112 Processing helix chain 'I' and resid 187 through 196 Processing helix chain 'J' and resid 52A through 55 removed outlier: 3.713A pdb=" N LEU J 55 " --> pdb=" O GLY J 52A" (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 52A through 55' Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.571A pdb=" N LYS J 64 " --> pdb=" O ASP J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 36 removed outlier: 3.568A pdb=" N GLY A 16 " --> pdb=" O GLY B 23 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS A 14 " --> pdb=" O HIS B 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 53 removed outlier: 5.329A pdb=" N LEU A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 60 removed outlier: 7.015A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ILE A 87 " --> pdb=" O ILE A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.544A pdb=" N GLU A 119 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.544A pdb=" N GLU A 119 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 176 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL A 178 " --> pdb=" O THR A 235 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 5.187A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A 146 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 287 through 288 removed outlier: 3.744A pdb=" N ILE A 288 " --> pdb=" O CYS A 281 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 302 " --> pdb=" O GLN A 282 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.583A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE H 107 " --> pdb=" O PHE H 90 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 17 through 19 removed outlier: 3.604A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.742A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.579A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 62 through 67 removed outlier: 3.594A pdb=" N THR L 74 " --> pdb=" O SER L 63 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER L 65 " --> pdb=" O THR L 72 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 22 through 24 removed outlier: 3.680A pdb=" N GLY D 16 " --> pdb=" O GLY C 23 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 25 through 26 removed outlier: 3.616A pdb=" N VAL D 34 " --> pdb=" O VAL D 26 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 39 through 41 Processing sheet with id=AC3, first strand: chain 'D' and resid 43 through 44 removed outlier: 3.524A pdb=" N GLN D 295 " --> pdb=" O LYS D 307 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 51 through 53 removed outlier: 5.360A pdb=" N LEU D 51 " --> pdb=" O ASP D 275 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N CYS D 277 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 59 through 60 removed outlier: 6.984A pdb=" N LEU D 59 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE D 87 " --> pdb=" O ILE D 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 118 through 119 removed outlier: 7.921A pdb=" N LEU D 179 " --> pdb=" O PRO D 254 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 118 through 119 removed outlier: 3.828A pdb=" N VAL D 178 " --> pdb=" O THR D 235 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 136 through 141 removed outlier: 5.223A pdb=" N CYS D 139 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER D 146 " --> pdb=" O CYS D 139 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 164 through 169 removed outlier: 3.559A pdb=" N ARG D 211 " --> pdb=" O VAL D 204 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR D 209 " --> pdb=" O SER D 206 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 286 through 288 removed outlier: 3.624A pdb=" N ILE D 288 " --> pdb=" O CYS D 281 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N CYS D 281 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE D 302 " --> pdb=" O GLN D 282 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.584A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 5 " --> pdb=" O LYS E 23 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.584A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 5 " --> pdb=" O LYS E 23 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER E 70 " --> pdb=" O TYR E 79 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.545A pdb=" N GLY E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE E 107 " --> pdb=" O PHE E 90 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL E 109 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU E 34 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N SER E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.984A pdb=" N THR F 5 " --> pdb=" O ARG F 24 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.508A pdb=" N LEU F 11 " --> pdb=" O ARG F 103 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR F 102 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR F 53 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 62 through 67 removed outlier: 3.660A pdb=" N THR F 74 " --> pdb=" O SER F 63 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER F 65 " --> pdb=" O THR F 72 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 22 through 24 removed outlier: 3.721A pdb=" N GLY I 16 " --> pdb=" O GLY G 23 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 131 through 132 Processing sheet with id=AE1, first strand: chain 'I' and resid 25 through 26 removed outlier: 3.562A pdb=" N VAL I 34 " --> pdb=" O VAL I 26 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 39 through 41 Processing sheet with id=AE3, first strand: chain 'I' and resid 43 through 44 Processing sheet with id=AE4, first strand: chain 'I' and resid 51 through 53 removed outlier: 5.323A pdb=" N LEU I 51 " --> pdb=" O ASP I 275 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N CYS I 277 " --> pdb=" O LEU I 51 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.986A pdb=" N LEU I 59 " --> pdb=" O VAL I 88 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ILE I 87 " --> pdb=" O ILE I 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'I' and resid 136 through 141 removed outlier: 5.242A pdb=" N CYS I 139 " --> pdb=" O SER I 146 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER I 146 " --> pdb=" O CYS I 139 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 151 through 153 removed outlier: 7.780A pdb=" N LEU I 179 " --> pdb=" O PRO I 254 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL I 178 " --> pdb=" O THR I 235 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG I 229 " --> pdb=" O HIS I 184 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 151 through 153 removed outlier: 7.780A pdb=" N LEU I 179 " --> pdb=" O PRO I 254 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 164 through 169 Processing sheet with id=AF1, first strand: chain 'I' and resid 281 through 282 removed outlier: 3.752A pdb=" N ILE I 302 " --> pdb=" O GLN I 282 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.614A pdb=" N LEU J 5 " --> pdb=" O LYS J 23 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU J 20 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER J 70 " --> pdb=" O TYR J 79 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.608A pdb=" N GLY J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE J 107 " --> pdb=" O PHE J 90 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL J 109 " --> pdb=" O ALA J 88 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL J 37 " --> pdb=" O TYR J 91 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.754A pdb=" N THR K 5 " --> pdb=" O ARG K 24 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.963A pdb=" N THR K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR K 102 " --> pdb=" O TYR K 86 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 62 through 67 removed outlier: 3.605A pdb=" N THR K 74 " --> pdb=" O SER K 63 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER K 65 " --> pdb=" O THR K 72 " (cutoff:3.500A) 529 hydrogen bonds defined for protein. 1455 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: 3.04 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5696 1.35 - 1.47: 4562 1.47 - 1.59: 7582 1.59 - 1.72: 1 1.72 - 1.84: 102 Bond restraints: 17943 Sorted by residual: bond pdb=" CB PRO D 306 " pdb=" CG PRO D 306 " ideal model delta sigma weight residual 1.492 1.619 -0.127 5.00e-02 4.00e+02 6.49e+00 bond pdb=" N GLY C 1 " pdb=" CA GLY C 1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.39e+00 bond pdb=" N GLY B 1 " pdb=" CA GLY B 1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.20e+00 bond pdb=" N GLY G 1 " pdb=" CA GLY G 1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.06e+00 bond pdb=" N GLU L 81 " pdb=" CA GLU L 81 " ideal model delta sigma weight residual 1.459 1.484 -0.026 1.28e-02 6.10e+03 4.00e+00 ... (remaining 17938 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 23810 2.11 - 4.23: 468 4.23 - 6.34: 44 6.34 - 8.45: 6 8.45 - 10.57: 2 Bond angle restraints: 24330 Sorted by residual: angle pdb=" CA PRO D 306 " pdb=" N PRO D 306 " pdb=" CD PRO D 306 " ideal model delta sigma weight residual 112.00 101.63 10.37 1.40e+00 5.10e-01 5.48e+01 angle pdb=" CA PRO D 99 " pdb=" N PRO D 99 " pdb=" CD PRO D 99 " ideal model delta sigma weight residual 112.00 105.53 6.47 1.40e+00 5.10e-01 2.14e+01 angle pdb=" CA PRO I 128 " pdb=" N PRO I 128 " pdb=" CD PRO I 128 " ideal model delta sigma weight residual 112.00 106.31 5.69 1.40e+00 5.10e-01 1.65e+01 angle pdb=" N VAL H 100A" pdb=" CA VAL H 100A" pdb=" C VAL H 100A" ideal model delta sigma weight residual 108.88 100.87 8.01 2.16e+00 2.14e-01 1.38e+01 angle pdb=" N PRO A 306 " pdb=" CA PRO A 306 " pdb=" C PRO A 306 " ideal model delta sigma weight residual 110.40 115.62 -5.22 1.61e+00 3.86e-01 1.05e+01 ... (remaining 24325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 8937 18.00 - 35.99: 1191 35.99 - 53.99: 256 53.99 - 71.98: 51 71.98 - 89.98: 14 Dihedral angle restraints: 10449 sinusoidal: 4182 harmonic: 6267 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 177.56 -84.56 1 1.00e+01 1.00e-02 8.69e+01 dihedral pdb=" CA VAL H 100A" pdb=" C VAL H 100A" pdb=" N PRO H 100B" pdb=" CA PRO H 100B" ideal model delta harmonic sigma weight residual 180.00 -138.88 -41.12 0 5.00e+00 4.00e-02 6.76e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 92 " pdb=" CB CYS E 92 " ideal model delta sinusoidal sigma weight residual -86.00 -153.61 67.61 1 1.00e+01 1.00e-02 5.94e+01 ... (remaining 10446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2265 0.054 - 0.108: 338 0.108 - 0.162: 96 0.162 - 0.216: 3 0.216 - 0.270: 4 Chirality restraints: 2706 Sorted by residual: chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 2703 not shown) Planarity restraints: 3141 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H 100A" 0.102 5.00e-02 4.00e+02 1.54e-01 3.79e+01 pdb=" N PRO H 100B" -0.266 5.00e-02 4.00e+02 pdb=" CA PRO H 100B" 0.085 5.00e-02 4.00e+02 pdb=" CD PRO H 100B" 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP I 127 " 0.090 5.00e-02 4.00e+02 1.33e-01 2.85e+01 pdb=" N PRO I 128 " -0.231 5.00e-02 4.00e+02 pdb=" CA PRO I 128 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO I 128 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 98 " -0.071 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO D 99 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " -0.056 5.00e-02 4.00e+02 ... (remaining 3138 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 345 2.63 - 3.20: 15720 3.20 - 3.77: 25317 3.77 - 4.33: 34424 4.33 - 4.90: 57327 Nonbonded interactions: 133133 Sorted by model distance: nonbonded pdb=" OG SER J 35 " pdb=" OG SER J 50 " model vdw 2.068 3.040 nonbonded pdb=" OG SER E 35 " pdb=" OG SER E 50 " model vdw 2.078 3.040 nonbonded pdb=" OG SER H 35 " pdb=" OG SER H 50 " model vdw 2.107 3.040 nonbonded pdb=" O3 NAG M 1 " pdb=" O5 NAG M 2 " model vdw 2.116 3.040 nonbonded pdb=" O3 NAG O 1 " pdb=" O5 NAG O 2 " model vdw 2.119 3.040 ... (remaining 133128 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 'D' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 1.690 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.880 Find NCS groups from input model: 0.460 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: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 18000 Z= 0.189 Angle : 0.696 10.566 24474 Z= 0.353 Chirality : 0.045 0.270 2706 Planarity : 0.007 0.154 3117 Dihedral : 16.464 89.976 6366 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.17 % Favored : 93.74 % Rotamer: Outliers : 0.64 % Allowed : 25.70 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.51 (0.18), residues: 2157 helix: 0.87 (0.28), residues: 372 sheet: -0.67 (0.27), residues: 375 loop : -1.72 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 229 TYR 0.016 0.001 TYR D 98 PHE 0.024 0.001 PHE G 110 TRP 0.017 0.001 TRP E 100E HIS 0.009 0.001 HIS G 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 (17943) covalent geometry : angle 0.68704 / 0.35 (24330) SS BOND : bond 0.00353 / 0.24 ( 27) SS BOND : angle 1.34295 / 0.83 ( 54) hydrogen bonds : bond 0.29671 / 19.71 ( 512) hydrogen bonds : angle 9.67093 / 7.10 ( 1455) link_BETA1-4 : bond 0.00401 / 0.28 ( 6) link_BETA1-4 : angle 2.00304 / 1.14 ( 18) link_NAG-ASN : bond 0.00216 / 0.11 ( 24) link_NAG-ASN : angle 1.69346 / 1.10 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 0.751 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: B 62 GLN cc_start: 0.9292 (tp40) cc_final: 0.8936 (mp10) REVERT: B 90 ASP cc_start: 0.9037 (m-30) cc_final: 0.8526 (m-30) REVERT: A 24 ASP cc_start: 0.9191 (m-30) cc_final: 0.8882 (t0) REVERT: H 13 ARG cc_start: 0.8900 (mtt90) cc_final: 0.8611 (mtt-85) REVERT: H 95 ASP cc_start: 0.8889 (t0) cc_final: 0.8326 (m-30) REVERT: L 32 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8600 (mt-10) REVERT: L 82 ASP cc_start: 0.7825 (m-30) cc_final: 0.6586 (m-30) REVERT: C 19 ASP cc_start: 0.9060 (m-30) cc_final: 0.8680 (p0) REVERT: C 62 GLN cc_start: 0.9371 (tp40) cc_final: 0.9073 (mp10) REVERT: C 149 MET cc_start: 0.9293 (tpp) cc_final: 0.8922 (tpp) REVERT: E 13 ARG cc_start: 0.9377 (mtp85) cc_final: 0.8687 (mtt-85) REVERT: E 95 ASP cc_start: 0.8823 (t0) cc_final: 0.8392 (m-30) REVERT: F 32 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8028 (mt-10) REVERT: F 75 ILE cc_start: 0.8484 (mt) cc_final: 0.8235 (mt) REVERT: F 78 LEU cc_start: 0.8043 (mp) cc_final: 0.7837 (tt) REVERT: G 90 ASP cc_start: 0.9149 (m-30) cc_final: 0.8841 (m-30) REVERT: G 149 MET cc_start: 0.9195 (tpp) cc_final: 0.8983 (tpp) REVERT: I 316 MET cc_start: 0.9345 (mtm) cc_final: 0.9076 (mpp) REVERT: J 75 GLN cc_start: 0.9512 (mt0) cc_final: 0.9168 (mp10) REVERT: J 95 ASP cc_start: 0.8851 (t0) cc_final: 0.8108 (m-30) REVERT: K 4 MET cc_start: 0.8685 (mpp) cc_final: 0.8463 (mmp) REVERT: K 75 ILE cc_start: 0.8491 (mt) cc_final: 0.8167 (mt) REVERT: K 78 LEU cc_start: 0.7989 (mp) cc_final: 0.7455 (mp) REVERT: K 86 TYR cc_start: 0.8289 (m-10) cc_final: 0.7953 (m-10) outliers start: 12 outliers final: 6 residues processed: 199 average time/residue: 0.1474 time to fit residues: 44.1314 Evaluate side-chains 106 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain G residue 169 ASN Chi-restraints excluded: chain I residue 136 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0040 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 overall best weight: 3.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 HIS B 60 ASN H 81 GLN L 27 GLN D 322 ASN ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 ASN I 231 ASN J 3 GLN J 81 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.043745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.032856 restraints weight = 114135.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.034026 restraints weight = 62808.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.034823 restraints weight = 43470.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.035360 restraints weight = 34152.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.035714 restraints weight = 29111.004| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18000 Z= 0.223 Angle : 0.729 9.250 24474 Z= 0.371 Chirality : 0.043 0.240 2706 Planarity : 0.006 0.147 3117 Dihedral : 4.761 40.056 2376 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.03 % Favored : 93.88 % Rotamer: Outliers : 3.97 % Allowed : 24.85 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 4.30 % 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: -1.32 (0.17), residues: 2157 helix: 1.14 (0.26), residues: 381 sheet: -0.34 (0.27), residues: 387 loop : -1.72 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 83 TYR 0.015 0.002 TYR E 79 PHE 0.020 0.002 PHE A 258 TRP 0.014 0.002 TRP I 153 HIS 0.007 0.001 HIS C 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (17943) covalent geometry : angle 0.71642 / 0.37 (24330) SS BOND : bond 0.00496 / 0.30 ( 27) SS BOND : angle 1.53715 / 1.06 ( 54) hydrogen bonds : bond 0.05730 / 3.83 ( 512) hydrogen bonds : angle 6.49485 / 4.76 ( 1455) link_BETA1-4 : bond 0.00220 / 0.15 ( 6) link_BETA1-4 : angle 1.79183 / 1.17 ( 18) link_NAG-ASN : bond 0.00391 / 0.24 ( 24) link_NAG-ASN : angle 2.13114 / 1.52 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 112 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 ASP cc_start: 0.8496 (p0) cc_final: 0.7792 (p0) REVERT: B 90 ASP cc_start: 0.9035 (m-30) cc_final: 0.8821 (m-30) REVERT: B 149 MET cc_start: 0.9203 (tpp) cc_final: 0.8748 (mmm) REVERT: A 24 ASP cc_start: 0.9289 (m-30) cc_final: 0.9034 (t0) REVERT: H 95 ASP cc_start: 0.8899 (t0) cc_final: 0.8397 (m-30) REVERT: L 32 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8584 (mt-10) REVERT: L 86 TYR cc_start: 0.8260 (m-10) cc_final: 0.7949 (m-10) REVERT: C 19 ASP cc_start: 0.9111 (m-30) cc_final: 0.8597 (p0) REVERT: C 149 MET cc_start: 0.9200 (tpp) cc_final: 0.8859 (tpp) REVERT: E 75 GLN cc_start: 0.9458 (mt0) cc_final: 0.9178 (mt0) REVERT: E 95 ASP cc_start: 0.8853 (t0) cc_final: 0.8383 (m-30) REVERT: F 78 LEU cc_start: 0.8283 (mp) cc_final: 0.7615 (mp) REVERT: G 149 MET cc_start: 0.9239 (tpp) cc_final: 0.8985 (tpp) REVERT: J 72 ASP cc_start: 0.8041 (t70) cc_final: 0.6629 (t70) REVERT: J 75 GLN cc_start: 0.9617 (mt0) cc_final: 0.9152 (mp10) REVERT: J 95 ASP cc_start: 0.8872 (t0) cc_final: 0.8179 (m-30) REVERT: K 86 TYR cc_start: 0.8353 (m-10) cc_final: 0.8035 (m-10) outliers start: 75 outliers final: 35 residues processed: 184 average time/residue: 0.1181 time to fit residues: 34.6520 Evaluate side-chains 126 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain C residue 146 ASN Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain G residue 128 ASN Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 205 optimal weight: 20.0000 chunk 143 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 186 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 62 GLN ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.042249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.031245 restraints weight = 116399.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.032375 restraints weight = 64850.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.033144 restraints weight = 45400.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.033659 restraints weight = 36043.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.033999 restraints weight = 30913.653| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18000 Z= 0.239 Angle : 0.713 11.059 24474 Z= 0.360 Chirality : 0.044 0.250 2706 Planarity : 0.006 0.146 3117 Dihedral : 4.854 39.247 2368 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.63 % Favored : 93.28 % Rotamer: Outliers : 5.41 % Allowed : 23.16 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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 (0.18), residues: 2157 helix: 1.31 (0.26), residues: 381 sheet: -0.60 (0.25), residues: 444 loop : -1.60 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 13 TYR 0.014 0.002 TYR I 168 PHE 0.016 0.002 PHE A 213 TRP 0.014 0.001 TRP I 153 HIS 0.006 0.001 HIS C 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.24 (17943) covalent geometry : angle 0.70014 / 0.36 (24330) SS BOND : bond 0.00524 / 0.31 ( 27) SS BOND : angle 1.71848 / 1.00 ( 54) hydrogen bonds : bond 0.05069 / 3.40 ( 512) hydrogen bonds : angle 6.01290 / 4.40 ( 1455) link_BETA1-4 : bond 0.00588 / 0.39 ( 6) link_BETA1-4 : angle 1.44389 / 0.97 ( 18) link_NAG-ASN : bond 0.00471 / 0.29 ( 24) link_NAG-ASN : angle 2.12227 / 1.50 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 98 time to evaluate : 0.651 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: B 77 MET cc_start: 0.8648 (mpp) cc_final: 0.8142 (tpp) REVERT: B 149 MET cc_start: 0.9127 (tpp) cc_final: 0.8845 (mmm) REVERT: A 24 ASP cc_start: 0.9352 (m-30) cc_final: 0.9018 (t0) REVERT: H 83 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.7164 (mpt180) REVERT: H 95 ASP cc_start: 0.8969 (t0) cc_final: 0.8289 (m-30) REVERT: L 4 MET cc_start: 0.8164 (mmm) cc_final: 0.7937 (mmm) REVERT: L 32 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8582 (mt-10) REVERT: C 77 MET cc_start: 0.8225 (mmt) cc_final: 0.7992 (mmt) REVERT: C 149 MET cc_start: 0.9215 (tpp) cc_final: 0.8802 (tpp) REVERT: E 72 ASP cc_start: 0.8045 (t70) cc_final: 0.7575 (t70) REVERT: E 75 GLN cc_start: 0.9501 (mt0) cc_final: 0.9183 (mt0) REVERT: E 95 ASP cc_start: 0.8887 (t0) cc_final: 0.8259 (m-30) REVERT: F 32 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8438 (mt-10) REVERT: F 75 ILE cc_start: 0.8429 (mp) cc_final: 0.7880 (tp) REVERT: G 149 MET cc_start: 0.9251 (tpp) cc_final: 0.8948 (tpp) REVERT: I 292 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8906 (mm) REVERT: J 75 GLN cc_start: 0.9638 (mt0) cc_final: 0.9145 (mp10) REVERT: J 95 ASP cc_start: 0.9019 (t0) cc_final: 0.8215 (m-30) outliers start: 102 outliers final: 62 residues processed: 192 average time/residue: 0.1142 time to fit residues: 35.1663 Evaluate side-chains 147 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 83 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 146 ASN Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 169 ASN Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 163 ASN Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 208 HIS Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 60 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 206 optimal weight: 1.9990 chunk 212 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 152 optimal weight: 0.9980 chunk 186 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.042613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.031709 restraints weight = 115092.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.032858 restraints weight = 63382.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.033635 restraints weight = 44025.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.034161 restraints weight = 34747.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.034514 restraints weight = 29685.902| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18000 Z= 0.162 Angle : 0.658 9.355 24474 Z= 0.326 Chirality : 0.043 0.250 2706 Planarity : 0.006 0.140 3117 Dihedral : 4.702 41.055 2366 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.52 % Favored : 94.39 % Rotamer: Outliers : 4.29 % Allowed : 24.43 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.92 (0.18), residues: 2157 helix: 1.74 (0.27), residues: 369 sheet: -0.46 (0.24), residues: 456 loop : -1.41 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 13 TYR 0.011 0.001 TYR K 86 PHE 0.018 0.001 PHE E 67 TRP 0.011 0.001 TRP I 153 HIS 0.004 0.001 HIS C 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (17943) covalent geometry : angle 0.64504 / 0.32 (24330) SS BOND : bond 0.00362 / 0.23 ( 27) SS BOND : angle 1.65372 / 1.06 ( 54) hydrogen bonds : bond 0.04410 / 2.95 ( 512) hydrogen bonds : angle 5.66752 / 4.15 ( 1455) link_BETA1-4 : bond 0.00531 / 0.34 ( 6) link_BETA1-4 : angle 1.42533 / 0.92 ( 18) link_NAG-ASN : bond 0.00290 / 0.17 ( 24) link_NAG-ASN : angle 1.99596 / 1.41 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 88 time to evaluate : 0.635 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: symmetry clash REVERT: B 2 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7821 (tt) REVERT: B 77 MET cc_start: 0.8544 (mpp) cc_final: 0.8121 (mmt) REVERT: B 149 MET cc_start: 0.9180 (tpp) cc_final: 0.8900 (mmm) REVERT: A 24 ASP cc_start: 0.9354 (m-30) cc_final: 0.9027 (t0) REVERT: A 278 ASP cc_start: 0.9013 (t0) cc_final: 0.8800 (t0) REVERT: H 95 ASP cc_start: 0.8920 (t0) cc_final: 0.8310 (m-30) REVERT: L 32 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8498 (mt-10) REVERT: C 14 TRP cc_start: 0.9318 (OUTLIER) cc_final: 0.8970 (m-90) REVERT: C 147 GLU cc_start: 0.9422 (OUTLIER) cc_final: 0.9215 (tp30) REVERT: C 149 MET cc_start: 0.9234 (tpp) cc_final: 0.8822 (tpp) REVERT: D 292 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9096 (mm) REVERT: E 95 ASP cc_start: 0.8913 (t0) cc_final: 0.8278 (m-30) REVERT: G 149 MET cc_start: 0.9258 (tpp) cc_final: 0.8927 (tpp) REVERT: I 199 ASN cc_start: 0.8998 (OUTLIER) cc_final: 0.8771 (p0) REVERT: I 292 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8894 (mm) REVERT: J 95 ASP cc_start: 0.8988 (t0) cc_final: 0.8210 (m-30) REVERT: K 86 TYR cc_start: 0.8450 (m-10) cc_final: 0.8093 (m-10) outliers start: 81 outliers final: 54 residues processed: 162 average time/residue: 0.1110 time to fit residues: 28.5942 Evaluate side-chains 142 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 82 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain C residue 14 TRP Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 30 CYS Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 169 ASN Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 163 ASN Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 208 HIS Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 200 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 150 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 118 optimal weight: 0.4980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.042723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.032113 restraints weight = 117238.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.033278 restraints weight = 64179.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.034075 restraints weight = 44264.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.034594 restraints weight = 34631.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.034956 restraints weight = 29551.957| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18000 Z= 0.115 Angle : 0.644 10.511 24474 Z= 0.316 Chirality : 0.043 0.248 2706 Planarity : 0.005 0.140 3117 Dihedral : 4.686 40.894 2366 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.19 % Favored : 94.71 % Rotamer: Outliers : 4.08 % Allowed : 23.32 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 4.30 % Twisted General : 0.05 % 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: -0.77 (0.18), residues: 2157 helix: 1.86 (0.27), residues: 369 sheet: -0.20 (0.24), residues: 456 loop : -1.38 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 13 TYR 0.011 0.001 TYR L 86 PHE 0.012 0.001 PHE D 118 TRP 0.008 0.001 TRP I 153 HIS 0.004 0.001 HIS C 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (17943) covalent geometry : angle 0.62868 / 0.31 (24330) SS BOND : bond 0.00325 / 0.21 ( 27) SS BOND : angle 2.10600 / 1.39 ( 54) hydrogen bonds : bond 0.04191 / 2.80 ( 512) hydrogen bonds : angle 5.52577 / 4.07 ( 1455) link_BETA1-4 : bond 0.00579 / 0.39 ( 6) link_BETA1-4 : angle 1.53990 / 0.97 ( 18) link_NAG-ASN : bond 0.00224 / 0.12 ( 24) link_NAG-ASN : angle 1.89910 / 1.34 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 100 time to evaluate : 0.532 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: symmetry clash revert: symmetry clash REVERT: B 2 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7825 (tt) REVERT: B 77 MET cc_start: 0.8590 (mpp) cc_final: 0.8136 (mmt) REVERT: B 149 MET cc_start: 0.9190 (tpp) cc_final: 0.8914 (mmm) REVERT: H 13 ARG cc_start: 0.8987 (mtt-85) cc_final: 0.8254 (mtt-85) REVERT: H 95 ASP cc_start: 0.8877 (t0) cc_final: 0.8324 (m-30) REVERT: L 32 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8442 (mt-10) REVERT: C 14 TRP cc_start: 0.9254 (OUTLIER) cc_final: 0.9012 (m-90) REVERT: C 149 MET cc_start: 0.9201 (tpp) cc_final: 0.8797 (tpp) REVERT: D 44 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7404 (tm-30) REVERT: D 292 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9084 (mm) REVERT: E 95 ASP cc_start: 0.8839 (t0) cc_final: 0.8288 (m-30) REVERT: G 74 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7724 (pt0) REVERT: G 147 GLU cc_start: 0.9389 (OUTLIER) cc_final: 0.9075 (tp30) REVERT: G 149 MET cc_start: 0.9183 (tpp) cc_final: 0.8884 (mmm) REVERT: I 199 ASN cc_start: 0.8925 (OUTLIER) cc_final: 0.8690 (p0) REVERT: I 292 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8924 (mm) REVERT: J 95 ASP cc_start: 0.8927 (t0) cc_final: 0.8187 (m-30) REVERT: K 6 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.6694 (pt0) REVERT: K 86 TYR cc_start: 0.8361 (m-10) cc_final: 0.7947 (m-10) outliers start: 77 outliers final: 48 residues processed: 174 average time/residue: 0.1145 time to fit residues: 31.7942 Evaluate side-chains 143 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 86 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain C residue 14 TRP Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 169 ASN Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 163 ASN Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 150 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 208 optimal weight: 20.0000 chunk 42 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 ASN A 199 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.041672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.031121 restraints weight = 117450.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.032245 restraints weight = 64932.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.032996 restraints weight = 44937.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.033518 restraints weight = 35480.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.033830 restraints weight = 30171.815| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18000 Z= 0.188 Angle : 0.662 9.391 24474 Z= 0.327 Chirality : 0.043 0.252 2706 Planarity : 0.005 0.142 3117 Dihedral : 4.628 43.373 2366 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.12 % Favored : 93.74 % Rotamer: Outliers : 4.93 % Allowed : 22.84 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.80 (0.18), residues: 2157 helix: 1.83 (0.27), residues: 372 sheet: -0.31 (0.24), residues: 456 loop : -1.37 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 13 TYR 0.016 0.001 TYR L 86 PHE 0.011 0.001 PHE A 213 TRP 0.010 0.001 TRP I 153 HIS 0.005 0.001 HIS C 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (17943) covalent geometry : angle 0.64815 / 0.32 (24330) SS BOND : bond 0.00434 / 0.30 ( 27) SS BOND : angle 1.82220 / 1.27 ( 54) hydrogen bonds : bond 0.04070 / 2.73 ( 512) hydrogen bonds : angle 5.40669 / 3.97 ( 1455) link_BETA1-4 : bond 0.00436 / 0.30 ( 6) link_BETA1-4 : angle 1.38082 / 0.93 ( 18) link_NAG-ASN : bond 0.00371 / 0.23 ( 24) link_NAG-ASN : angle 2.00117 / 1.41 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 89 time to evaluate : 0.700 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: symmetry clash revert: symmetry clash REVERT: B 2 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7794 (tt) REVERT: B 77 MET cc_start: 0.8605 (mpp) cc_final: 0.8116 (mmt) REVERT: B 149 MET cc_start: 0.9141 (tpp) cc_final: 0.8922 (mmm) REVERT: H 95 ASP cc_start: 0.8982 (t0) cc_final: 0.8399 (m-30) REVERT: L 32 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8535 (mt-10) REVERT: C 149 MET cc_start: 0.9206 (tpp) cc_final: 0.8861 (tpp) REVERT: E 75 GLN cc_start: 0.9613 (mt0) cc_final: 0.9363 (mp10) REVERT: E 95 ASP cc_start: 0.8867 (t0) cc_final: 0.8349 (m-30) REVERT: G 74 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7740 (pt0) REVERT: G 147 GLU cc_start: 0.9392 (OUTLIER) cc_final: 0.9148 (tp30) REVERT: G 149 MET cc_start: 0.9189 (tpp) cc_final: 0.8857 (tpp) REVERT: I 199 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.8701 (p0) REVERT: I 278 ASP cc_start: 0.9023 (t0) cc_final: 0.8708 (t0) REVERT: I 292 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8904 (mm) REVERT: J 95 ASP cc_start: 0.8951 (t0) cc_final: 0.8190 (m-30) REVERT: K 6 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.6986 (pt0) REVERT: K 86 TYR cc_start: 0.8389 (m-10) cc_final: 0.8173 (m-10) outliers start: 93 outliers final: 76 residues processed: 172 average time/residue: 0.1082 time to fit residues: 30.4123 Evaluate side-chains 166 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 84 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 277 CYS Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 169 ASN Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 163 ASN Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 208 HIS Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 192 optimal weight: 6.9990 chunk 209 optimal weight: 20.0000 chunk 165 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS F 6 GLN ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.041420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.031287 restraints weight = 115035.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.032399 restraints weight = 63644.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.033156 restraints weight = 44076.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.033666 restraints weight = 34739.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.034017 restraints weight = 29517.994| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18000 Z= 0.165 Angle : 0.645 9.647 24474 Z= 0.317 Chirality : 0.043 0.251 2706 Planarity : 0.006 0.140 3117 Dihedral : 4.565 39.077 2366 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.75 % Favored : 94.11 % Rotamer: Outliers : 5.09 % Allowed : 23.11 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.77 (0.18), residues: 2157 helix: 1.88 (0.27), residues: 372 sheet: -0.29 (0.24), residues: 456 loop : -1.36 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 13 TYR 0.017 0.001 TYR L 86 PHE 0.012 0.001 PHE D 118 TRP 0.010 0.001 TRP I 153 HIS 0.004 0.001 HIS C 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (17943) covalent geometry : angle 0.63173 / 0.31 (24330) SS BOND : bond 0.00459 / 0.31 ( 27) SS BOND : angle 1.69940 / 1.00 ( 54) hydrogen bonds : bond 0.03983 / 2.66 ( 512) hydrogen bonds : angle 5.34203 / 3.94 ( 1455) link_BETA1-4 : bond 0.00504 / 0.35 ( 6) link_BETA1-4 : angle 1.37588 / 0.93 ( 18) link_NAG-ASN : bond 0.00307 / 0.19 ( 24) link_NAG-ASN : angle 1.94514 / 1.37 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 88 time to evaluate : 0.562 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: symmetry clash REVERT: B 2 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7832 (tt) REVERT: B 77 MET cc_start: 0.8588 (mpp) cc_final: 0.8155 (mmt) REVERT: B 149 MET cc_start: 0.9195 (tpp) cc_final: 0.8953 (mmm) REVERT: H 46 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8110 (mm-30) REVERT: H 95 ASP cc_start: 0.8939 (t0) cc_final: 0.8360 (m-30) REVERT: L 32 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8472 (mt-10) REVERT: C 14 TRP cc_start: 0.9266 (OUTLIER) cc_final: 0.8980 (m-90) REVERT: C 149 MET cc_start: 0.9194 (tpp) cc_final: 0.8733 (tpp) REVERT: D 292 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9103 (mm) REVERT: E 75 GLN cc_start: 0.9621 (mt0) cc_final: 0.9362 (mp10) REVERT: E 95 ASP cc_start: 0.8871 (t0) cc_final: 0.8627 (t0) REVERT: G 147 GLU cc_start: 0.9360 (OUTLIER) cc_final: 0.9135 (tp30) REVERT: G 149 MET cc_start: 0.9178 (tpp) cc_final: 0.8902 (mmm) REVERT: I 199 ASN cc_start: 0.8921 (OUTLIER) cc_final: 0.8687 (p0) REVERT: I 292 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8924 (mm) REVERT: J 95 ASP cc_start: 0.8946 (t0) cc_final: 0.8176 (m-30) REVERT: K 6 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7276 (pt0) REVERT: K 86 TYR cc_start: 0.8389 (m-10) cc_final: 0.8176 (m-10) outliers start: 96 outliers final: 73 residues processed: 175 average time/residue: 0.1068 time to fit residues: 30.6283 Evaluate side-chains 164 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 84 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain C residue 14 TRP Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 169 ASN Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 163 ASN Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 208 HIS Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 136 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 199 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 HIS ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.041597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.031464 restraints weight = 114561.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.032585 restraints weight = 62361.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.033347 restraints weight = 42935.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.033868 restraints weight = 33683.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.034226 restraints weight = 28569.049| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 18000 Z= 0.137 Angle : 0.638 11.708 24474 Z= 0.314 Chirality : 0.043 0.252 2706 Planarity : 0.005 0.129 3117 Dihedral : 4.489 35.705 2364 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.80 % Favored : 94.07 % Rotamer: Outliers : 4.77 % Allowed : 23.21 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.73 (0.18), residues: 2157 helix: 1.92 (0.27), residues: 372 sheet: -0.25 (0.24), residues: 456 loop : -1.34 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 13 TYR 0.017 0.001 TYR L 86 PHE 0.011 0.001 PHE D 118 TRP 0.014 0.001 TRP B 14 HIS 0.004 0.001 HIS C 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (17943) covalent geometry : angle 0.62239 / 0.31 (24330) SS BOND : bond 0.00322 / 0.20 ( 27) SS BOND : angle 2.14599 / 1.32 ( 54) hydrogen bonds : bond 0.03893 / 2.60 ( 512) hydrogen bonds : angle 5.33294 / 3.92 ( 1455) link_BETA1-4 : bond 0.00478 / 0.33 ( 6) link_BETA1-4 : angle 1.38781 / 0.93 ( 18) link_NAG-ASN : bond 0.00258 / 0.16 ( 24) link_NAG-ASN : angle 1.88190 / 1.32 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 86 time to evaluate : 0.540 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: symmetry clash REVERT: B 2 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7707 (tt) REVERT: B 77 MET cc_start: 0.8536 (mpp) cc_final: 0.8093 (mmt) REVERT: B 149 MET cc_start: 0.9216 (tpp) cc_final: 0.8956 (mmm) REVERT: H 46 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8114 (mm-30) REVERT: H 95 ASP cc_start: 0.8943 (t0) cc_final: 0.8347 (m-30) REVERT: L 32 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8466 (mt-10) REVERT: C 14 TRP cc_start: 0.9235 (OUTLIER) cc_final: 0.8980 (m-90) REVERT: C 149 MET cc_start: 0.9088 (tpp) cc_final: 0.8768 (tpp) REVERT: D 283 THR cc_start: 0.9507 (OUTLIER) cc_final: 0.9219 (p) REVERT: D 292 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9089 (mm) REVERT: E 75 GLN cc_start: 0.9629 (mt0) cc_final: 0.9382 (mp10) REVERT: E 95 ASP cc_start: 0.8907 (t0) cc_final: 0.8386 (m-30) REVERT: G 147 GLU cc_start: 0.9364 (OUTLIER) cc_final: 0.9139 (tp30) REVERT: G 149 MET cc_start: 0.9194 (tpp) cc_final: 0.8907 (mmm) REVERT: I 199 ASN cc_start: 0.8934 (OUTLIER) cc_final: 0.8702 (p0) REVERT: I 292 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8908 (mm) REVERT: J 95 ASP cc_start: 0.8952 (t0) cc_final: 0.8162 (m-30) REVERT: K 6 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7269 (pt0) outliers start: 90 outliers final: 75 residues processed: 168 average time/residue: 0.0993 time to fit residues: 27.6090 Evaluate side-chains 164 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 81 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain C residue 14 TRP Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 169 ASN Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 163 ASN Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 208 HIS Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 139 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 193 optimal weight: 5.9990 chunk 211 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 ASN L 6 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN L 89 GLN F 6 GLN ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 ASN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.040730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.030260 restraints weight = 119294.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.031320 restraints weight = 67681.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.032040 restraints weight = 47652.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.032528 restraints weight = 37911.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.032845 restraints weight = 32533.940| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 18000 Z= 0.258 Angle : 0.713 11.254 24474 Z= 0.354 Chirality : 0.044 0.256 2706 Planarity : 0.006 0.131 3117 Dihedral : 4.729 33.694 2364 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.32 % Favored : 92.54 % Rotamer: Outliers : 4.93 % Allowed : 23.05 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.90 (0.18), residues: 2157 helix: 1.92 (0.26), residues: 384 sheet: -0.53 (0.25), residues: 438 loop : -1.46 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 13 TYR 0.023 0.002 TYR L 86 PHE 0.014 0.002 PHE A 213 TRP 0.018 0.002 TRP I 153 HIS 0.009 0.001 HIS I 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.26 (17943) covalent geometry : angle 0.69589 / 0.35 (24330) SS BOND : bond 0.00613 / 0.39 ( 27) SS BOND : angle 2.46399 / 1.85 ( 54) hydrogen bonds : bond 0.04063 / 2.74 ( 512) hydrogen bonds : angle 5.48230 / 4.03 ( 1455) link_BETA1-4 : bond 0.00367 / 0.24 ( 6) link_BETA1-4 : angle 1.33325 / 0.93 ( 18) link_NAG-ASN : bond 0.00515 / 0.33 ( 24) link_NAG-ASN : angle 2.07678 / 1.45 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 80 time to evaluate : 0.660 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: B 2 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7716 (tt) REVERT: B 77 MET cc_start: 0.8608 (mpp) cc_final: 0.8183 (mmt) REVERT: B 149 MET cc_start: 0.9169 (tpp) cc_final: 0.8923 (mmm) REVERT: H 95 ASP cc_start: 0.8979 (t0) cc_final: 0.8331 (m-30) REVERT: L 32 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8567 (mt-10) REVERT: C 149 MET cc_start: 0.9065 (tpp) cc_final: 0.8682 (tpp) REVERT: D 292 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9129 (mm) REVERT: E 75 GLN cc_start: 0.9633 (mt0) cc_final: 0.9381 (mp10) REVERT: E 82 MET cc_start: 0.8211 (mtt) cc_final: 0.7790 (mpp) REVERT: E 95 ASP cc_start: 0.8923 (t0) cc_final: 0.8369 (m-30) REVERT: F 32 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8426 (mt-10) REVERT: F 105 GLU cc_start: 0.7385 (tm-30) cc_final: 0.7128 (tm-30) REVERT: G 147 GLU cc_start: 0.9388 (OUTLIER) cc_final: 0.9184 (tp30) REVERT: G 149 MET cc_start: 0.9218 (tpp) cc_final: 0.8881 (tpp) REVERT: I 199 ASN cc_start: 0.8918 (OUTLIER) cc_final: 0.8667 (p0) REVERT: I 292 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8984 (mm) REVERT: J 95 ASP cc_start: 0.8963 (t0) cc_final: 0.8149 (m-30) REVERT: K 6 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.7588 (pt0) outliers start: 93 outliers final: 78 residues processed: 165 average time/residue: 0.1023 time to fit residues: 27.7548 Evaluate side-chains 162 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 78 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 169 ASN Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 163 ASN Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 208 HIS Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 277 CYS Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 106 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 169 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 149 optimal weight: 0.9990 chunk 201 optimal weight: 0.8980 chunk 122 optimal weight: 20.0000 chunk 139 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 60 ASN A 199 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 ASN ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.041201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.030912 restraints weight = 114307.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.032015 restraints weight = 62909.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.032771 restraints weight = 43596.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.033274 restraints weight = 34333.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.033618 restraints weight = 29345.732| |-----------------------------------------------------------------------------| r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 18000 Z= 0.154 Angle : 0.662 11.640 24474 Z= 0.325 Chirality : 0.043 0.256 2706 Planarity : 0.005 0.129 3117 Dihedral : 4.545 32.442 2364 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.56 % Favored : 94.30 % Rotamer: Outliers : 4.40 % Allowed : 23.79 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.78 (0.18), residues: 2157 helix: 1.97 (0.27), residues: 372 sheet: -0.35 (0.24), residues: 456 loop : -1.38 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 13 TYR 0.023 0.001 TYR L 86 PHE 0.021 0.001 PHE G 140 TRP 0.013 0.001 TRP I 153 HIS 0.004 0.001 HIS G 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (17943) covalent geometry : angle 0.65075 / 0.32 (24330) SS BOND : bond 0.00348 / 0.22 ( 27) SS BOND : angle 1.59836 / 1.09 ( 54) hydrogen bonds : bond 0.03931 / 2.63 ( 512) hydrogen bonds : angle 5.30327 / 3.91 ( 1455) link_BETA1-4 : bond 0.00401 / 0.27 ( 6) link_BETA1-4 : angle 1.32830 / 0.92 ( 18) link_NAG-ASN : bond 0.00307 / 0.19 ( 24) link_NAG-ASN : angle 1.91133 / 1.33 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 85 time to evaluate : 0.622 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: B 2 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7725 (tt) REVERT: B 77 MET cc_start: 0.8521 (mpp) cc_final: 0.8116 (mmt) REVERT: B 149 MET cc_start: 0.9195 (tpp) cc_final: 0.8933 (mmm) REVERT: H 95 ASP cc_start: 0.8954 (t0) cc_final: 0.8513 (t70) REVERT: L 32 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8518 (mt-10) REVERT: L 82 ASP cc_start: 0.8013 (m-30) cc_final: 0.7691 (m-30) REVERT: C 149 MET cc_start: 0.9080 (tpp) cc_final: 0.8760 (tpp) REVERT: D 225 ASP cc_start: 0.8726 (t0) cc_final: 0.8465 (t0) REVERT: D 292 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9100 (mm) REVERT: E 75 GLN cc_start: 0.9604 (mt0) cc_final: 0.9352 (mp10) REVERT: E 95 ASP cc_start: 0.8929 (t0) cc_final: 0.8673 (t0) REVERT: F 32 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8350 (mt-10) REVERT: F 86 TYR cc_start: 0.8367 (m-10) cc_final: 0.8155 (m-10) REVERT: F 105 GLU cc_start: 0.7386 (tm-30) cc_final: 0.7138 (tm-30) REVERT: G 147 GLU cc_start: 0.9381 (OUTLIER) cc_final: 0.9162 (tp30) REVERT: G 149 MET cc_start: 0.9199 (tpp) cc_final: 0.8965 (mmm) REVERT: I 292 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8990 (mm) REVERT: J 95 ASP cc_start: 0.8913 (t0) cc_final: 0.8104 (m-30) REVERT: K 6 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.7548 (pt0) outliers start: 83 outliers final: 70 residues processed: 162 average time/residue: 0.1041 time to fit residues: 27.4651 Evaluate side-chains 156 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 81 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 163 ASN Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 208 HIS Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 67 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 84 optimal weight: 0.0970 chunk 174 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.042552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.031775 restraints weight = 114260.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.032933 restraints weight = 62556.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.033723 restraints weight = 43148.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.034252 restraints weight = 33894.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.034608 restraints weight = 28872.856| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 18000 Z= 0.114 Angle : 0.648 11.506 24474 Z= 0.315 Chirality : 0.043 0.250 2706 Planarity : 0.005 0.127 3117 Dihedral : 4.490 32.517 2364 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.01 % Favored : 94.85 % Rotamer: Outliers : 3.34 % Allowed : 24.80 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.05 % 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: -0.67 (0.18), residues: 2157 helix: 1.96 (0.26), residues: 372 sheet: 0.08 (0.25), residues: 426 loop : -1.40 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 13 TYR 0.019 0.001 TYR L 86 PHE 0.010 0.001 PHE D 118 TRP 0.012 0.001 TRP H 100E HIS 0.004 0.001 HIS C 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (17943) covalent geometry : angle 0.63482 / 0.31 (24330) SS BOND : bond 0.00441 / 0.21 ( 27) SS BOND : angle 1.95558 / 1.30 ( 54) hydrogen bonds : bond 0.03788 / 2.53 ( 512) hydrogen bonds : angle 5.34077 / 3.91 ( 1455) link_BETA1-4 : bond 0.00587 / 0.38 ( 6) link_BETA1-4 : angle 1.49565 / 1.01 ( 18) link_NAG-ASN : bond 0.00220 / 0.12 ( 24) link_NAG-ASN : angle 1.79412 / 1.26 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2478.16 seconds wall clock time: 44 minutes 5.07 seconds (2645.07 seconds total)