Starting phenix.real_space_refine on Thu Mar 5 00:44:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d21_27139/03_2026/8d21_27139.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d21_27139/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d21_27139/03_2026/8d21_27139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d21_27139/03_2026/8d21_27139.map" model { file = "/net/cci-nas-00/data/ceres_data/8d21_27139/03_2026/8d21_27139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d21_27139/03_2026/8d21_27139.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 21 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 dihedrals: 21 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 dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 3.58, per 1000 atoms: 0.20 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: 1.53 Conformation dependent library (CDL) restraints added in 661.3 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: 0.83 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: 3.09 Time building geometry restraints manager: 1.97 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 - 21.52: 9846 21.52 - 43.03: 1006 43.03 - 64.55: 154 64.55 - 86.06: 54 86.06 - 107.58: 13 Dihedral angle restraints: 11073 sinusoidal: 4806 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 11070 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: 0.00 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: 2.000 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.160 Find NCS groups from input model: 0.300 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 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 : 17.327 107.581 6990 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 covalent geometry : bond 0.00417 (17943) covalent geometry : angle 0.68704 (24330) SS BOND : bond 0.00353 ( 27) SS BOND : angle 1.34295 ( 54) hydrogen bonds : bond 0.29671 ( 512) hydrogen bonds : angle 9.67093 ( 1455) link_BETA1-4 : bond 0.00401 ( 6) link_BETA1-4 : angle 2.00304 ( 18) link_NAG-ASN : bond 0.00216 ( 24) link_NAG-ASN : angle 1.69346 ( 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 : 0.731 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: 0.1461 time to fit residues: 43.6086 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 : 0.633 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 81 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.043565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.032512 restraints weight = 114185.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.033682 restraints weight = 63217.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.034474 restraints weight = 43978.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.035012 restraints weight = 34755.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.035376 restraints weight = 29703.872| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18000 Z= 0.222 Angle : 0.735 9.169 24474 Z= 0.371 Chirality : 0.043 0.234 2706 Planarity : 0.006 0.147 3117 Dihedral : 8.895 61.858 3000 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.26 % Favored : 93.65 % Rotamer: Outliers : 4.19 % Allowed : 24.54 % 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: -1.35 (0.17), residues: 2157 helix: 1.10 (0.26), residues: 381 sheet: -0.47 (0.26), residues: 393 loop : -1.71 (0.15), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 66 TYR 0.015 0.002 TYR E 79 PHE 0.020 0.002 PHE A 258 TRP 0.016 0.002 TRP I 153 HIS 0.008 0.001 HIS C 25 Details of bonding type rmsd covalent geometry : bond 0.00485 (17943) covalent geometry : angle 0.72139 (24330) SS BOND : bond 0.00466 ( 27) SS BOND : angle 1.51463 ( 54) hydrogen bonds : bond 0.05531 ( 512) hydrogen bonds : angle 6.41355 ( 1455) link_BETA1-4 : bond 0.00387 ( 6) link_BETA1-4 : angle 2.37631 ( 18) link_NAG-ASN : bond 0.00446 ( 24) link_NAG-ASN : angle 2.17540 ( 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 194 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 115 time to evaluate : 0.629 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: B 19 ASP cc_start: 0.8494 (p0) cc_final: 0.7811 (p0) REVERT: B 149 MET cc_start: 0.9212 (tpp) cc_final: 0.8740 (mmm) REVERT: A 24 ASP cc_start: 0.9297 (m-30) cc_final: 0.9033 (t0) REVERT: H 95 ASP cc_start: 0.8913 (t0) cc_final: 0.8375 (m-30) REVERT: L 32 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8597 (mt-10) REVERT: L 86 TYR cc_start: 0.8277 (m-10) cc_final: 0.7975 (m-10) REVERT: C 19 ASP cc_start: 0.9157 (m-30) cc_final: 0.8622 (p0) REVERT: C 149 MET cc_start: 0.9224 (tpp) cc_final: 0.8860 (tpp) REVERT: E 75 GLN cc_start: 0.9468 (mt0) cc_final: 0.9172 (mp10) REVERT: E 95 ASP cc_start: 0.8876 (t0) cc_final: 0.8376 (m-30) REVERT: F 78 LEU cc_start: 0.8326 (mp) cc_final: 0.7655 (mp) REVERT: G 149 MET cc_start: 0.9249 (tpp) cc_final: 0.8982 (tpp) REVERT: J 72 ASP cc_start: 0.8098 (t70) cc_final: 0.6740 (t70) REVERT: J 75 GLN cc_start: 0.9627 (mt0) cc_final: 0.9169 (mp10) REVERT: J 95 ASP cc_start: 0.8907 (t0) cc_final: 0.8199 (m-30) REVERT: K 86 TYR cc_start: 0.8376 (m-10) cc_final: 0.8070 (m-10) outliers start: 79 outliers final: 40 residues processed: 192 average time/residue: 0.1187 time to fit residues: 36.4184 Evaluate side-chains 129 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 89 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 H residue 100 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 48 ILE 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 65 SER Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 98 TYR 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: 0.9990 chunk 191 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 186 optimal weight: 30.0000 chunk 34 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3105 r_free = 0.3105 target = 0.042360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.031389 restraints weight = 115614.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.032535 restraints weight = 64015.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.033310 restraints weight = 44590.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.033831 restraints weight = 35291.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.034172 restraints weight = 30183.839| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18000 Z= 0.231 Angle : 0.717 12.541 24474 Z= 0.361 Chirality : 0.044 0.245 2706 Planarity : 0.006 0.146 3117 Dihedral : 7.748 59.119 2992 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.49 % Favored : 93.42 % Rotamer: Outliers : 5.19 % Allowed : 23.48 % Favored : 71.33 % 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: -1.18 (0.18), residues: 2157 helix: 1.36 (0.26), residues: 381 sheet: -0.58 (0.25), residues: 444 loop : -1.58 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 13 TYR 0.013 0.002 TYR I 168 PHE 0.016 0.002 PHE E 67 TRP 0.013 0.001 TRP I 153 HIS 0.006 0.001 HIS C 25 Details of bonding type rmsd covalent geometry : bond 0.00500 (17943) covalent geometry : angle 0.70203 (24330) SS BOND : bond 0.00474 ( 27) SS BOND : angle 1.90075 ( 54) hydrogen bonds : bond 0.05098 ( 512) hydrogen bonds : angle 5.98479 ( 1455) link_BETA1-4 : bond 0.00801 ( 6) link_BETA1-4 : angle 2.06927 ( 18) link_NAG-ASN : bond 0.00440 ( 24) link_NAG-ASN : angle 2.08998 ( 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 195 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 97 time to evaluate : 0.655 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: B 149 MET cc_start: 0.9159 (tpp) cc_final: 0.8882 (mmm) REVERT: A 24 ASP cc_start: 0.9350 (m-30) cc_final: 0.9091 (t0) REVERT: H 83 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.7092 (mpt180) REVERT: H 95 ASP cc_start: 0.8927 (t0) cc_final: 0.8307 (m-30) REVERT: L 4 MET cc_start: 0.8153 (mmm) cc_final: 0.7926 (mmm) REVERT: L 32 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8537 (mt-10) REVERT: C 149 MET cc_start: 0.9220 (tpp) cc_final: 0.8813 (tpp) REVERT: E 75 GLN cc_start: 0.9537 (mt0) cc_final: 0.9308 (mp10) REVERT: E 95 ASP cc_start: 0.8882 (t0) cc_final: 0.8258 (m-30) REVERT: F 32 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8426 (mt-10) REVERT: F 75 ILE cc_start: 0.8429 (mp) cc_final: 0.7876 (tp) REVERT: G 149 MET cc_start: 0.9251 (tpp) cc_final: 0.8957 (tpp) REVERT: I 292 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8889 (mm) REVERT: J 75 GLN cc_start: 0.9625 (mt0) cc_final: 0.9119 (mp10) REVERT: J 95 ASP cc_start: 0.9007 (t0) cc_final: 0.8216 (m-30) outliers start: 98 outliers final: 56 residues processed: 187 average time/residue: 0.1249 time to fit residues: 37.3183 Evaluate side-chains 141 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 83 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 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 I residue 317 VAL 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: 0.9980 chunk 172 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 206 optimal weight: 1.9990 chunk 212 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 chunk 186 optimal weight: 40.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.043502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.032562 restraints weight = 114218.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.033742 restraints weight = 62408.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.034526 restraints weight = 43144.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.035073 restraints weight = 34095.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.035437 restraints weight = 29037.228| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18000 Z= 0.120 Angle : 0.656 9.553 24474 Z= 0.322 Chirality : 0.044 0.243 2706 Planarity : 0.005 0.141 3117 Dihedral : 7.159 59.946 2990 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.33 % Favored : 94.58 % Rotamer: Outliers : 3.66 % Allowed : 24.17 % Favored : 72.18 % 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: -0.90 (0.18), residues: 2157 helix: 1.52 (0.27), residues: 381 sheet: -0.27 (0.24), residues: 465 loop : -1.44 (0.17), residues: 1311 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 0.015 0.001 PHE E 67 TRP 0.009 0.001 TRP I 153 HIS 0.004 0.001 HIS C 25 Details of bonding type rmsd covalent geometry : bond 0.00269 (17943) covalent geometry : angle 0.64082 (24330) SS BOND : bond 0.00569 ( 27) SS BOND : angle 1.90724 ( 54) hydrogen bonds : bond 0.04486 ( 512) hydrogen bonds : angle 5.67439 ( 1455) link_BETA1-4 : bond 0.00540 ( 6) link_BETA1-4 : angle 2.10970 ( 18) link_NAG-ASN : bond 0.00213 ( 24) link_NAG-ASN : angle 1.94337 ( 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 165 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 96 time to evaluate : 0.605 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 2 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7802 (tt) REVERT: B 149 MET cc_start: 0.9170 (tpp) cc_final: 0.8855 (mmm) REVERT: A 24 ASP cc_start: 0.9361 (m-30) cc_final: 0.9022 (t0) REVERT: A 225 ASP cc_start: 0.8703 (t70) cc_final: 0.8406 (t0) REVERT: A 278 ASP cc_start: 0.9094 (t0) cc_final: 0.8884 (t0) REVERT: H 13 ARG cc_start: 0.8933 (mtt-85) cc_final: 0.8148 (mtt-85) REVERT: H 83 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.7248 (mpt180) REVERT: H 95 ASP cc_start: 0.8915 (t0) cc_final: 0.8232 (m-30) REVERT: L 32 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8424 (mt-10) REVERT: C 14 TRP cc_start: 0.9264 (OUTLIER) cc_final: 0.8946 (m-90) REVERT: C 147 GLU cc_start: 0.9409 (OUTLIER) cc_final: 0.9193 (tp30) REVERT: C 149 MET cc_start: 0.9209 (tpp) cc_final: 0.8763 (tpp) REVERT: D 292 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9047 (mm) REVERT: E 75 GLN cc_start: 0.9541 (mt0) cc_final: 0.9293 (mp10) REVERT: E 95 ASP cc_start: 0.8850 (t0) cc_final: 0.8229 (m-30) REVERT: G 59 MET cc_start: 0.8751 (tpp) cc_final: 0.8539 (tpp) REVERT: G 147 GLU cc_start: 0.9450 (OUTLIER) cc_final: 0.9138 (tp30) REVERT: G 149 MET cc_start: 0.9230 (tpp) cc_final: 0.9002 (mmm) REVERT: I 199 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8756 (p0) REVERT: I 292 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8841 (mm) REVERT: J 75 GLN cc_start: 0.9775 (mt0) cc_final: 0.9337 (mp10) REVERT: J 95 ASP cc_start: 0.8974 (t0) cc_final: 0.8199 (m-30) outliers start: 69 outliers final: 41 residues processed: 161 average time/residue: 0.1237 time to fit residues: 32.0964 Evaluate side-chains 133 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 84 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 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 H residue 83 ARG 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 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 269 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL 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 18 HIS Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 115 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 283 THR Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 200 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 159 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.041715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.031376 restraints weight = 114800.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.032475 restraints weight = 64606.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.033224 restraints weight = 45244.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.033726 restraints weight = 35853.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.034074 restraints weight = 30716.730| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18000 Z= 0.192 Angle : 0.677 9.477 24474 Z= 0.334 Chirality : 0.043 0.249 2706 Planarity : 0.006 0.142 3117 Dihedral : 7.088 59.575 2990 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.40 % Favored : 93.46 % Rotamer: Outliers : 5.03 % Allowed : 22.68 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.86 (0.18), residues: 2157 helix: 1.83 (0.27), residues: 372 sheet: -0.38 (0.24), residues: 471 loop : -1.42 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 13 TYR 0.012 0.001 TYR G 94 PHE 0.015 0.001 PHE E 67 TRP 0.010 0.001 TRP I 153 HIS 0.005 0.001 HIS C 25 Details of bonding type rmsd covalent geometry : bond 0.00426 (17943) covalent geometry : angle 0.65963 (24330) SS BOND : bond 0.00322 ( 27) SS BOND : angle 2.27331 ( 54) hydrogen bonds : bond 0.04316 ( 512) hydrogen bonds : angle 5.61752 ( 1455) link_BETA1-4 : bond 0.00681 ( 6) link_BETA1-4 : angle 1.66107 ( 18) link_NAG-ASN : bond 0.00377 ( 24) link_NAG-ASN : angle 2.00575 ( 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 186 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 91 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: symmetry clash REVERT: B 2 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7774 (tt) REVERT: B 77 MET cc_start: 0.8028 (mmt) cc_final: 0.7639 (mmt) REVERT: B 149 MET cc_start: 0.9176 (tpp) cc_final: 0.8915 (mmm) REVERT: A 24 ASP cc_start: 0.9328 (m-30) cc_final: 0.9107 (t0) REVERT: H 13 ARG cc_start: 0.8972 (mtt-85) cc_final: 0.8147 (mtt-85) REVERT: H 83 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7426 (mpt180) REVERT: H 95 ASP cc_start: 0.8948 (t0) cc_final: 0.8382 (m-30) REVERT: L 32 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8529 (mt-10) REVERT: C 77 MET cc_start: 0.8128 (mmt) cc_final: 0.7315 (mmt) REVERT: C 149 MET cc_start: 0.9215 (tpp) cc_final: 0.8841 (tpp) REVERT: D 44 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7549 (tm-30) REVERT: E 72 ASP cc_start: 0.7803 (p0) cc_final: 0.7277 (p0) REVERT: E 75 GLN cc_start: 0.9551 (mt0) cc_final: 0.9231 (mp10) REVERT: E 95 ASP cc_start: 0.8865 (t0) cc_final: 0.8286 (m-30) REVERT: G 149 MET cc_start: 0.9229 (tpp) cc_final: 0.8921 (tpp) REVERT: I 199 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8674 (p0) REVERT: I 278 ASP cc_start: 0.9044 (t0) cc_final: 0.8612 (t0) REVERT: I 292 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8917 (mm) REVERT: J 95 ASP cc_start: 0.8942 (t0) cc_final: 0.8219 (m-30) REVERT: K 6 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.6917 (pt0) REVERT: K 86 TYR cc_start: 0.8506 (m-10) cc_final: 0.8103 (m-10) outliers start: 95 outliers final: 68 residues processed: 179 average time/residue: 0.1184 time to fit residues: 34.2761 Evaluate side-chains 159 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 85 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 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 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 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 78 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 30 CYS Chi-restraints excluded: chain D residue 44 GLU 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 269 THR 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 73 LEU Chi-restraints excluded: chain F residue 75 ILE 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 150 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 208 optimal weight: 0.7980 chunk 42 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN B 146 ASN L 37 GLN K 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.041463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.030899 restraints weight = 117559.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.032005 restraints weight = 65060.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.032763 restraints weight = 45251.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.033261 restraints weight = 35713.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.033611 restraints weight = 30607.042| |-----------------------------------------------------------------------------| r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18000 Z= 0.193 Angle : 0.669 9.448 24474 Z= 0.330 Chirality : 0.043 0.251 2706 Planarity : 0.006 0.146 3117 Dihedral : 6.836 57.182 2988 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.75 % Favored : 94.11 % Rotamer: Outliers : 5.30 % Allowed : 22.79 % Favored : 71.91 % 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: -0.82 (0.18), residues: 2157 helix: 1.87 (0.27), residues: 372 sheet: -0.38 (0.24), residues: 456 loop : -1.38 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 13 TYR 0.013 0.001 TYR G 94 PHE 0.013 0.001 PHE D 118 TRP 0.011 0.001 TRP I 153 HIS 0.005 0.001 HIS C 25 Details of bonding type rmsd covalent geometry : bond 0.00424 (17943) covalent geometry : angle 0.65534 (24330) SS BOND : bond 0.00425 ( 27) SS BOND : angle 1.81752 ( 54) hydrogen bonds : bond 0.04127 ( 512) hydrogen bonds : angle 5.45031 ( 1455) link_BETA1-4 : bond 0.00402 ( 6) link_BETA1-4 : angle 1.52562 ( 18) link_NAG-ASN : bond 0.00360 ( 24) link_NAG-ASN : angle 2.00673 ( 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 190 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 90 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: symmetry clash REVERT: B 2 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7811 (tt) REVERT: B 77 MET cc_start: 0.8008 (mmt) cc_final: 0.7544 (mmt) REVERT: B 149 MET cc_start: 0.9179 (tpp) cc_final: 0.8920 (mmm) REVERT: A 24 ASP cc_start: 0.9345 (m-30) cc_final: 0.9136 (t0) REVERT: A 278 ASP cc_start: 0.9130 (t0) cc_final: 0.8762 (t0) REVERT: H 95 ASP cc_start: 0.8950 (t0) cc_final: 0.8363 (m-30) REVERT: L 32 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8531 (mt-10) REVERT: C 14 TRP cc_start: 0.9312 (OUTLIER) cc_final: 0.8991 (m-90) REVERT: C 77 MET cc_start: 0.8262 (mmt) cc_final: 0.7566 (mmt) REVERT: C 149 MET cc_start: 0.9192 (tpp) cc_final: 0.8729 (tpp) REVERT: D 292 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9165 (mm) REVERT: E 72 ASP cc_start: 0.7965 (p0) cc_final: 0.7189 (p0) REVERT: E 75 GLN cc_start: 0.9584 (mt0) cc_final: 0.9223 (mp10) REVERT: E 95 ASP cc_start: 0.8863 (t0) cc_final: 0.8345 (m-30) REVERT: F 32 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8424 (mt-10) REVERT: G 77 MET cc_start: 0.8742 (tpp) cc_final: 0.8240 (tpp) REVERT: G 147 GLU cc_start: 0.9384 (OUTLIER) cc_final: 0.9169 (tp30) REVERT: G 149 MET cc_start: 0.9220 (tpp) cc_final: 0.8941 (mmm) REVERT: I 199 ASN cc_start: 0.8928 (OUTLIER) cc_final: 0.8691 (p0) REVERT: I 292 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8917 (mm) REVERT: J 95 ASP cc_start: 0.8952 (t0) cc_final: 0.8190 (m-30) REVERT: K 6 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7260 (pt0) REVERT: K 86 TYR cc_start: 0.8475 (m-10) cc_final: 0.8204 (m-10) outliers start: 100 outliers final: 72 residues processed: 183 average time/residue: 0.1124 time to fit residues: 33.6515 Evaluate side-chains 166 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 87 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 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 14 TRP 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 146 ASN 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 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 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 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 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 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 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 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 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: 10.0000 chunk 165 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN D 183 HIS F 6 GLN ** G 43 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 = 0.3084 r_free = 0.3084 target = 0.040971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.030850 restraints weight = 115246.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.031942 restraints weight = 63961.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.032698 restraints weight = 44517.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.033206 restraints weight = 35008.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.033551 restraints weight = 29789.926| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18000 Z= 0.198 Angle : 0.669 9.444 24474 Z= 0.332 Chirality : 0.043 0.252 2706 Planarity : 0.006 0.149 3117 Dihedral : 6.655 55.941 2988 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.72 % Favored : 93.14 % Rotamer: Outliers : 4.93 % Allowed : 23.26 % 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: -0.82 (0.18), residues: 2157 helix: 1.88 (0.27), residues: 372 sheet: -0.40 (0.24), residues: 456 loop : -1.37 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 13 TYR 0.011 0.001 TYR A 168 PHE 0.012 0.001 PHE D 118 TRP 0.011 0.001 TRP A 153 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00436 (17943) covalent geometry : angle 0.65697 (24330) SS BOND : bond 0.00483 ( 27) SS BOND : angle 1.58049 ( 54) hydrogen bonds : bond 0.04053 ( 512) hydrogen bonds : angle 5.34212 ( 1455) link_BETA1-4 : bond 0.00485 ( 6) link_BETA1-4 : angle 1.46045 ( 18) link_NAG-ASN : bond 0.00370 ( 24) link_NAG-ASN : angle 2.02602 ( 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 180 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 87 time to evaluate : 0.707 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: B 2 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7843 (tt) REVERT: B 149 MET cc_start: 0.9154 (tpp) cc_final: 0.8934 (mmm) REVERT: A 24 ASP cc_start: 0.9373 (m-30) cc_final: 0.9140 (t0) REVERT: H 95 ASP cc_start: 0.8972 (t0) cc_final: 0.8358 (m-30) REVERT: L 4 MET cc_start: 0.8059 (mmm) cc_final: 0.7706 (mmm) REVERT: L 32 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8516 (mt-10) REVERT: C 14 TRP cc_start: 0.9316 (OUTLIER) cc_final: 0.8987 (m-90) REVERT: C 149 MET cc_start: 0.9077 (tpp) cc_final: 0.8738 (tpp) REVERT: D 292 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9159 (mm) REVERT: E 75 GLN cc_start: 0.9606 (mt0) cc_final: 0.9307 (mp10) REVERT: E 95 ASP cc_start: 0.8884 (t0) cc_final: 0.8342 (m-30) REVERT: F 32 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8429 (mt-10) REVERT: G 149 MET cc_start: 0.9218 (tpp) cc_final: 0.8948 (mmm) REVERT: I 199 ASN cc_start: 0.8923 (OUTLIER) cc_final: 0.8686 (p0) REVERT: I 292 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8927 (mm) REVERT: J 95 ASP cc_start: 0.8962 (t0) cc_final: 0.8188 (m-30) REVERT: K 6 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7403 (pt0) REVERT: K 86 TYR cc_start: 0.8458 (m-10) cc_final: 0.8244 (m-10) outliers start: 93 outliers final: 77 residues processed: 170 average time/residue: 0.1187 time to fit residues: 33.1157 Evaluate side-chains 162 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 79 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 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 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 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 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 179 LEU Chi-restraints excluded: chain D residue 204 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 13 VAL 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 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 115 VAL 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 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: 2.9990 chunk 26 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 143 optimal weight: 10.0000 chunk 188 optimal weight: 0.0870 chunk 124 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 199 optimal weight: 7.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.041997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.031398 restraints weight = 113101.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.032534 restraints weight = 62086.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.033300 restraints weight = 43039.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.033827 restraints weight = 34056.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.034174 restraints weight = 29091.518| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 18000 Z= 0.135 Angle : 0.654 10.789 24474 Z= 0.321 Chirality : 0.043 0.280 2706 Planarity : 0.005 0.145 3117 Dihedral : 6.490 55.894 2988 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.29 % Favored : 94.58 % Rotamer: Outliers : 4.72 % Allowed : 22.95 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.76 (0.18), residues: 2157 helix: 1.93 (0.27), residues: 372 sheet: -0.27 (0.24), residues: 456 loop : -1.37 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 13 TYR 0.009 0.001 TYR G 162 PHE 0.012 0.001 PHE D 118 TRP 0.009 0.001 TRP K 35 HIS 0.004 0.001 HIS C 25 Details of bonding type rmsd covalent geometry : bond 0.00308 (17943) covalent geometry : angle 0.63598 (24330) SS BOND : bond 0.00296 ( 27) SS BOND : angle 2.43148 ( 54) hydrogen bonds : bond 0.03944 ( 512) hydrogen bonds : angle 5.34738 ( 1455) link_BETA1-4 : bond 0.00536 ( 6) link_BETA1-4 : angle 1.56384 ( 18) link_NAG-ASN : bond 0.00240 ( 24) link_NAG-ASN : angle 1.91130 ( 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 173 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 84 time to evaluate : 0.724 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: B 2 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7838 (tt) REVERT: B 77 MET cc_start: 0.7900 (mmt) cc_final: 0.7426 (mmt) REVERT: B 149 MET cc_start: 0.9200 (tpp) cc_final: 0.8945 (mmm) REVERT: A 24 ASP cc_start: 0.9382 (m-30) cc_final: 0.9179 (t0) REVERT: H 95 ASP cc_start: 0.8948 (t0) cc_final: 0.8495 (t70) REVERT: L 4 MET cc_start: 0.8075 (mmm) cc_final: 0.7710 (mmm) REVERT: L 32 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8451 (mt-10) REVERT: C 14 TRP cc_start: 0.9249 (OUTLIER) cc_final: 0.8970 (m-90) REVERT: C 77 MET cc_start: 0.8582 (mmt) cc_final: 0.7773 (mmt) REVERT: C 149 MET cc_start: 0.9074 (tpp) cc_final: 0.8753 (tpp) REVERT: D 292 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9128 (mm) REVERT: E 75 GLN cc_start: 0.9611 (mt0) cc_final: 0.9303 (mp10) REVERT: E 95 ASP cc_start: 0.8908 (t0) cc_final: 0.8367 (m-30) REVERT: F 32 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8379 (mt-10) REVERT: G 149 MET cc_start: 0.9226 (tpp) cc_final: 0.8991 (mmm) REVERT: I 199 ASN cc_start: 0.8952 (OUTLIER) cc_final: 0.8724 (p0) REVERT: I 292 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8903 (mm) REVERT: J 95 ASP cc_start: 0.8962 (t0) cc_final: 0.8619 (t70) REVERT: K 6 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7325 (pt0) REVERT: K 86 TYR cc_start: 0.8476 (m-10) cc_final: 0.8261 (m-10) outliers start: 89 outliers final: 72 residues processed: 166 average time/residue: 0.1145 time to fit residues: 31.5421 Evaluate side-chains 159 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 81 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 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 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 14 TRP 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 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 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 68 THR 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 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 65 SER Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 131 THR 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 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: 10.0000 chunk 122 optimal weight: 20.0000 chunk 44 optimal weight: 30.0000 chunk 206 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 211 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 HIS L 79 GLN L 92 ASN F 6 GLN F 79 GLN G 43 ASN G 169 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.039942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.029562 restraints weight = 119981.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.030606 restraints weight = 67007.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.031327 restraints weight = 46947.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.031802 restraints weight = 37200.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.032130 restraints weight = 31972.614| |-----------------------------------------------------------------------------| r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 18000 Z= 0.387 Angle : 0.851 11.947 24474 Z= 0.423 Chirality : 0.047 0.271 2706 Planarity : 0.007 0.151 3117 Dihedral : 7.021 55.888 2988 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.25 % Favored : 91.56 % Rotamer: Outliers : 5.09 % Allowed : 23.00 % Favored : 71.91 % 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: -1.23 (0.18), residues: 2157 helix: 1.63 (0.26), residues: 384 sheet: -0.86 (0.24), residues: 447 loop : -1.63 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 13 TYR 0.032 0.003 TYR L 86 PHE 0.021 0.002 PHE A 213 TRP 0.019 0.002 TRP I 153 HIS 0.011 0.002 HIS I 184 Details of bonding type rmsd covalent geometry : bond 0.00834 (17943) covalent geometry : angle 0.83145 (24330) SS BOND : bond 0.00518 ( 27) SS BOND : angle 2.75567 ( 54) hydrogen bonds : bond 0.04478 ( 512) hydrogen bonds : angle 5.75318 ( 1455) link_BETA1-4 : bond 0.00433 ( 6) link_BETA1-4 : angle 1.20619 ( 18) link_NAG-ASN : bond 0.00860 ( 24) link_NAG-ASN : angle 2.51785 ( 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 172 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 76 time to evaluate : 0.745 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 2 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7661 (tt) REVERT: A 24 ASP cc_start: 0.9417 (m-30) cc_final: 0.9194 (t0) REVERT: A 199 ASN cc_start: 0.8876 (OUTLIER) cc_final: 0.8644 (p0) REVERT: H 95 ASP cc_start: 0.9068 (t0) cc_final: 0.8675 (t70) REVERT: L 32 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8532 (mt-10) REVERT: C 77 MET cc_start: 0.8664 (mmt) cc_final: 0.7951 (mmt) REVERT: C 149 MET cc_start: 0.9021 (tpp) cc_final: 0.8621 (tpp) REVERT: D 292 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9168 (mm) REVERT: E 75 GLN cc_start: 0.9590 (mt0) cc_final: 0.9279 (mp10) REVERT: E 95 ASP cc_start: 0.8961 (t0) cc_final: 0.8741 (t0) REVERT: F 32 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8411 (mt-10) REVERT: F 86 TYR cc_start: 0.8452 (m-10) cc_final: 0.8073 (m-10) REVERT: G 59 MET cc_start: 0.8942 (tpp) cc_final: 0.8167 (tmm) REVERT: G 149 MET cc_start: 0.9197 (tpp) cc_final: 0.8848 (tpp) REVERT: I 199 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8698 (p0) REVERT: I 292 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8930 (mm) REVERT: I 316 MET cc_start: 0.9410 (mtm) cc_final: 0.9168 (mpp) REVERT: J 95 ASP cc_start: 0.8988 (t0) cc_final: 0.8195 (m-30) REVERT: K 6 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.7770 (pt0) REVERT: K 32 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8398 (mt-10) outliers start: 96 outliers final: 79 residues processed: 167 average time/residue: 0.1099 time to fit residues: 30.5797 Evaluate side-chains 158 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 73 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 56 ILE Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 115 VAL 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 199 ASN 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 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 19 ASP Chi-restraints excluded: chain C residue 98 LEU 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 104 ASP 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 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 74 GLU 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 12 THR Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 30 CYS 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 104 ASP Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 131 THR 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 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 74 THR 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: 1.9990 chunk 19 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 201 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 39 optimal weight: 0.0030 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN F 6 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.041284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.031163 restraints weight = 112827.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.032256 restraints weight = 62819.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.033002 restraints weight = 43766.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.033504 restraints weight = 34554.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.033845 restraints weight = 29477.614| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18000 Z= 0.121 Angle : 0.676 10.154 24474 Z= 0.332 Chirality : 0.044 0.245 2706 Planarity : 0.005 0.144 3117 Dihedral : 6.447 55.555 2988 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.01 % Favored : 94.85 % Rotamer: Outliers : 3.44 % Allowed : 24.85 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % 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: -0.82 (0.18), residues: 2157 helix: 1.93 (0.27), residues: 372 sheet: -0.20 (0.24), residues: 441 loop : -1.47 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 170 TYR 0.014 0.001 TYR L 86 PHE 0.022 0.001 PHE G 140 TRP 0.014 0.002 TRP I 153 HIS 0.004 0.001 HIS I 183 Details of bonding type rmsd covalent geometry : bond 0.00269 (17943) covalent geometry : angle 0.66540 (24330) SS BOND : bond 0.00415 ( 27) SS BOND : angle 1.56495 ( 54) hydrogen bonds : bond 0.04020 ( 512) hydrogen bonds : angle 5.39158 ( 1455) link_BETA1-4 : bond 0.00495 ( 6) link_BETA1-4 : angle 1.51529 ( 18) link_NAG-ASN : bond 0.00238 ( 24) link_NAG-ASN : angle 1.84483 ( 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 149 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 84 time to evaluate : 0.691 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 2 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7900 (tt) REVERT: A 60 GLN cc_start: 0.8938 (mp10) cc_final: 0.8653 (mp10) REVERT: H 95 ASP cc_start: 0.8926 (t0) cc_final: 0.8503 (t70) REVERT: L 32 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8382 (mt-10) REVERT: C 149 MET cc_start: 0.9097 (tpp) cc_final: 0.8816 (tpp) REVERT: D 225 ASP cc_start: 0.8663 (t0) cc_final: 0.8396 (t0) REVERT: D 283 THR cc_start: 0.9526 (OUTLIER) cc_final: 0.9257 (p) REVERT: D 292 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9156 (mm) REVERT: E 66 ARG cc_start: 0.7782 (tpp80) cc_final: 0.7525 (tpp80) REVERT: E 75 GLN cc_start: 0.9594 (mt0) cc_final: 0.9304 (mp10) REVERT: E 95 ASP cc_start: 0.8922 (t0) cc_final: 0.8378 (m-30) REVERT: F 6 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7763 (pt0) REVERT: F 32 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8284 (mt-10) REVERT: F 86 TYR cc_start: 0.8363 (m-10) cc_final: 0.8047 (m-10) REVERT: G 149 MET cc_start: 0.9237 (tpp) cc_final: 0.9015 (mmm) REVERT: I 292 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8977 (mm) REVERT: J 75 GLN cc_start: 0.9741 (mt0) cc_final: 0.9511 (mt0) REVERT: J 95 ASP cc_start: 0.8893 (t0) cc_final: 0.8577 (t70) outliers start: 65 outliers final: 54 residues processed: 145 average time/residue: 0.1150 time to fit residues: 27.6379 Evaluate side-chains 136 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 77 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 30 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 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 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 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 52 CYS Chi-restraints excluded: chain D residue 56 ILE 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 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 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 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 76 CYS Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 131 THR 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 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 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: 7.9990 chunk 194 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 40 optimal weight: 0.5980 chunk 90 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN F 6 GLN G 169 ASN ** K 37 GLN ** 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 = 0.3066 r_free = 0.3066 target = 0.041115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.030581 restraints weight = 115913.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.031719 restraints weight = 63320.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.032477 restraints weight = 43620.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.032988 restraints weight = 34290.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.033336 restraints weight = 29230.181| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18000 Z= 0.128 Angle : 0.662 11.120 24474 Z= 0.323 Chirality : 0.043 0.247 2706 Planarity : 0.005 0.142 3117 Dihedral : 6.254 55.682 2988 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.24 % Favored : 94.62 % Rotamer: Outliers : 3.29 % Allowed : 24.80 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % 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: 1.96 (0.27), residues: 372 sheet: -0.36 (0.24), residues: 456 loop : -1.35 (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 0.018 0.001 PHE G 140 TRP 0.009 0.001 TRP I 153 HIS 0.005 0.001 HIS G 142 Details of bonding type rmsd covalent geometry : bond 0.00289 (17943) covalent geometry : angle 0.64987 (24330) SS BOND : bond 0.00609 ( 27) SS BOND : angle 1.67882 ( 54) hydrogen bonds : bond 0.03888 ( 512) hydrogen bonds : angle 5.22352 ( 1455) link_BETA1-4 : bond 0.00451 ( 6) link_BETA1-4 : angle 1.57186 ( 18) link_NAG-ASN : bond 0.00255 ( 24) link_NAG-ASN : angle 1.83537 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2640.51 seconds wall clock time: 46 minutes 48.68 seconds (2808.68 seconds total)