Starting phenix.real_space_refine on Sun Jun 15 20:44:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d21_27139/06_2025/8d21_27139.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d21_27139/06_2025/8d21_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_27139/06_2025/8d21_27139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d21_27139/06_2025/8d21_27139.map" model { file = "/net/cci-nas-00/data/ceres_data/8d21_27139/06_2025/8d21_27139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d21_27139/06_2025/8d21_27139.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.78, per 1000 atoms: 0.61 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: 4.28 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.30 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: 5.34 Time building geometry restraints manager: 5.11 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 39.700 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.380 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.017 0.001 TRP E 100E HIS 0.009 0.001 HIS G 25 PHE 0.024 0.001 PHE G 110 TYR 0.016 0.001 TYR D 98 ARG 0.009 0.001 ARG D 229 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 24) link_NAG-ASN : angle 1.69346 ( 72) link_BETA1-4 : bond 0.00401 ( 6) link_BETA1-4 : angle 2.00304 ( 18) hydrogen bonds : bond 0.29671 ( 512) hydrogen bonds : angle 9.67093 ( 1455) SS BOND : bond 0.00353 ( 27) SS BOND : angle 1.34295 ( 54) covalent geometry : bond 0.00417 (17943) covalent geometry : angle 0.68704 (24330) *********************** 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 : 1.993 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: B 62 GLN cc_start: 0.9292 (tp40) cc_final: 0.8938 (mp10) REVERT: B 90 ASP cc_start: 0.9037 (m-30) cc_final: 0.8374 (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: 0.8325 (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: 0.9082 (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: 0.8689 (mtt-85) REVERT: E 95 ASP cc_start: 0.8823 (t0) cc_final: 0.8394 (m-30) REVERT: F 32 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8029 (mt-10) REVERT: G 90 ASP cc_start: 0.9149 (m-30) cc_final: 0.8847 (m-30) REVERT: G 149 MET cc_start: 0.9195 (tpp) cc_final: 0.8984 (tpp) REVERT: I 316 MET cc_start: 0.9345 (mtm) cc_final: 0.9077 (mpp) REVERT: J 75 GLN cc_start: 0.9512 (mt0) cc_final: 0.9158 (mp10) REVERT: J 95 ASP cc_start: 0.8851 (t0) cc_final: 0.8109 (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: 0.7454 (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: 0.3398 time to fit residues: 101.0208 Evaluate side-chains 104 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 2.020 ------------------------------------------------------------------------------- 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 179 optimal weight: 0.9980 chunk 161 optimal weight: 0.3980 chunk 89 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 166 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 193 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** I 231 ASN J 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.045558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.034672 restraints weight = 111217.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.035912 restraints weight = 59870.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.036743 restraints weight = 40747.038| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18000 Z= 0.135 Angle : 0.702 9.185 24474 Z= 0.350 Chirality : 0.043 0.229 2706 Planarity : 0.006 0.143 3117 Dihedral : 8.649 61.303 3000 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.87 % Favored : 95.04 % Rotamer: Outliers : 2.91 % Allowed : 25.12 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.17), residues: 2157 helix: 1.08 (0.26), residues: 381 sheet: -0.16 (0.27), residues: 393 loop : -1.66 (0.15), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 153 HIS 0.007 0.001 HIS C 25 PHE 0.015 0.001 PHE A 258 TYR 0.015 0.001 TYR E 79 ARG 0.011 0.001 ARG E 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 24) link_NAG-ASN : angle 2.04416 ( 72) link_BETA1-4 : bond 0.00373 ( 6) link_BETA1-4 : angle 2.57940 ( 18) hydrogen bonds : bond 0.05808 ( 512) hydrogen bonds : angle 6.44555 ( 1455) SS BOND : bond 0.00498 ( 27) SS BOND : angle 1.38385 ( 54) covalent geometry : bond 0.00293 (17943) covalent geometry : angle 0.68891 (24330) *********************** 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 184 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 129 time to evaluate : 1.840 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: B 19 ASP cc_start: 0.8489 (p0) cc_final: 0.7870 (p0) REVERT: B 62 GLN cc_start: 0.9241 (tp40) cc_final: 0.8840 (mp10) REVERT: B 90 ASP cc_start: 0.9051 (m-30) cc_final: 0.8664 (m-30) REVERT: B 149 MET cc_start: 0.9237 (tpp) cc_final: 0.8649 (mmm) REVERT: A 24 ASP cc_start: 0.9252 (m-30) cc_final: 0.8961 (t0) REVERT: H 95 ASP cc_start: 0.8860 (t0) cc_final: 0.8269 (m-30) REVERT: L 32 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8602 (mt-10) REVERT: C 19 ASP cc_start: 0.9149 (m-30) cc_final: 0.8679 (p0) REVERT: C 62 GLN cc_start: 0.9289 (tp40) cc_final: 0.8884 (mp10) REVERT: C 149 MET cc_start: 0.9220 (tpp) cc_final: 0.8883 (tpp) REVERT: E 13 ARG cc_start: 0.9403 (mtp85) cc_final: 0.8671 (mtt-85) REVERT: E 72 ASP cc_start: 0.7853 (t70) cc_final: 0.7363 (t0) REVERT: E 75 GLN cc_start: 0.9452 (mt0) cc_final: 0.9133 (mt0) REVERT: E 95 ASP cc_start: 0.8825 (t0) cc_final: 0.8335 (m-30) REVERT: F 82 ASP cc_start: 0.7908 (m-30) cc_final: 0.7631 (m-30) REVERT: G 59 MET cc_start: 0.8702 (tpp) cc_final: 0.8447 (mmp) REVERT: G 90 ASP cc_start: 0.9254 (m-30) cc_final: 0.9000 (m-30) REVERT: G 149 MET cc_start: 0.9229 (tpp) cc_final: 0.8974 (tpp) REVERT: I 292 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8837 (mm) REVERT: J 72 ASP cc_start: 0.8171 (t70) cc_final: 0.6793 (t70) REVERT: J 75 GLN cc_start: 0.9591 (mt0) cc_final: 0.9123 (mp10) REVERT: J 95 ASP cc_start: 0.8888 (t0) cc_final: 0.8182 (m-30) outliers start: 55 outliers final: 23 residues processed: 180 average time/residue: 0.2696 time to fit residues: 76.1650 Evaluate side-chains 126 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 146 ASN Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 98 TYR 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 146 ASN Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 43 optimal weight: 5.9990 chunk 89 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 186 optimal weight: 20.0000 chunk 134 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 ASN ** G 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.043240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.032287 restraints weight = 113878.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.033440 restraints weight = 63035.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.034226 restraints weight = 43893.190| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18000 Z= 0.200 Angle : 0.693 10.923 24474 Z= 0.343 Chirality : 0.043 0.246 2706 Planarity : 0.006 0.146 3117 Dihedral : 7.453 58.479 2990 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.12 % Favored : 93.79 % Rotamer: Outliers : 4.08 % Allowed : 23.53 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.18), residues: 2157 helix: 1.38 (0.26), residues: 381 sheet: -0.36 (0.25), residues: 444 loop : -1.53 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 153 HIS 0.006 0.001 HIS C 25 PHE 0.014 0.002 PHE E 67 TYR 0.013 0.002 TYR A 195 ARG 0.007 0.001 ARG H 13 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 24) link_NAG-ASN : angle 2.05620 ( 72) link_BETA1-4 : bond 0.00565 ( 6) link_BETA1-4 : angle 2.13533 ( 18) hydrogen bonds : bond 0.05033 ( 512) hydrogen bonds : angle 5.92453 ( 1455) SS BOND : bond 0.00357 ( 27) SS BOND : angle 1.43779 ( 54) covalent geometry : bond 0.00436 (17943) covalent geometry : angle 0.67998 (24330) *********************** 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 179 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 102 time to evaluate : 2.569 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 77 MET cc_start: 0.8723 (mpp) cc_final: 0.8167 (tpp) REVERT: B 149 MET cc_start: 0.9145 (tpp) cc_final: 0.8821 (mmm) REVERT: A 24 ASP cc_start: 0.9333 (m-30) cc_final: 0.9104 (t0) REVERT: H 95 ASP cc_start: 0.8934 (t0) cc_final: 0.8373 (m-30) REVERT: L 32 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8616 (mt-10) REVERT: C 149 MET cc_start: 0.9244 (tpp) cc_final: 0.8878 (tpp) REVERT: E 72 ASP cc_start: 0.7885 (t70) cc_final: 0.7420 (t70) REVERT: E 75 GLN cc_start: 0.9470 (mt0) cc_final: 0.9129 (mt0) REVERT: E 95 ASP cc_start: 0.8868 (t0) cc_final: 0.8324 (m-30) REVERT: F 82 ASP cc_start: 0.8054 (m-30) cc_final: 0.7770 (m-30) REVERT: G 149 MET cc_start: 0.9269 (tpp) cc_final: 0.8994 (tpp) REVERT: J 75 GLN cc_start: 0.9618 (mt0) cc_final: 0.9119 (mp10) REVERT: J 95 ASP cc_start: 0.8955 (t0) cc_final: 0.8269 (m-30) outliers start: 77 outliers final: 48 residues processed: 173 average time/residue: 0.3560 time to fit residues: 100.7080 Evaluate side-chains 133 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 85 time to evaluate : 2.308 ------------------------------------------------------------------------------- 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 56 ILE Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain C residue 146 ASN Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 104 ASP 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 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 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 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 214 THR Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain J residue 68 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 107 optimal weight: 0.0570 chunk 35 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 102 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 38 optimal weight: 0.0170 chunk 204 optimal weight: 10.0000 chunk 142 optimal weight: 0.8980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.044448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.033691 restraints weight = 112529.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.034928 restraints weight = 59719.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.035761 restraints weight = 40312.858| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 18000 Z= 0.113 Angle : 0.641 11.263 24474 Z= 0.314 Chirality : 0.043 0.237 2706 Planarity : 0.005 0.140 3117 Dihedral : 6.847 58.842 2990 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.87 % Favored : 95.04 % Rotamer: Outliers : 3.02 % Allowed : 24.11 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.18), residues: 2157 helix: 1.49 (0.27), residues: 381 sheet: 0.03 (0.26), residues: 438 loop : -1.44 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 153 HIS 0.003 0.001 HIS C 25 PHE 0.016 0.001 PHE E 67 TYR 0.010 0.001 TYR B 119 ARG 0.007 0.000 ARG H 13 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 24) link_NAG-ASN : angle 1.92203 ( 72) link_BETA1-4 : bond 0.00638 ( 6) link_BETA1-4 : angle 2.12850 ( 18) hydrogen bonds : bond 0.04423 ( 512) hydrogen bonds : angle 5.67408 ( 1455) SS BOND : bond 0.00296 ( 27) SS BOND : angle 1.83946 ( 54) covalent geometry : bond 0.00248 (17943) covalent geometry : angle 0.62548 (24330) *********************** 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: 57 poor density : 108 time to evaluate : 1.701 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: symmetry clash REVERT: B 2 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7671 (tt) REVERT: B 77 MET cc_start: 0.8791 (mpp) cc_final: 0.8322 (mmt) REVERT: B 149 MET cc_start: 0.9186 (tpp) cc_final: 0.8857 (mmm) REVERT: A 24 ASP cc_start: 0.9355 (m-30) cc_final: 0.9111 (t0) REVERT: A 225 ASP cc_start: 0.8765 (t70) cc_final: 0.8464 (t0) REVERT: H 95 ASP cc_start: 0.8895 (t0) cc_final: 0.8306 (m-30) REVERT: L 4 MET cc_start: 0.8091 (mmm) cc_final: 0.7575 (mmm) REVERT: L 32 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8426 (mt-10) REVERT: C 147 GLU cc_start: 0.9393 (OUTLIER) cc_final: 0.9177 (tp30) REVERT: C 149 MET cc_start: 0.9199 (tpp) cc_final: 0.8845 (tpp) REVERT: D 283 THR cc_start: 0.9426 (OUTLIER) cc_final: 0.9154 (p) REVERT: D 292 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8990 (mm) REVERT: E 72 ASP cc_start: 0.8047 (t70) cc_final: 0.7594 (t70) REVERT: E 75 GLN cc_start: 0.9461 (mt0) cc_final: 0.9125 (mt0) REVERT: E 95 ASP cc_start: 0.8830 (t0) cc_final: 0.8319 (m-30) REVERT: F 82 ASP cc_start: 0.8165 (m-30) cc_final: 0.7824 (m-30) REVERT: G 77 MET cc_start: 0.8537 (mmt) cc_final: 0.8212 (mmt) REVERT: G 147 GLU cc_start: 0.9435 (OUTLIER) cc_final: 0.9099 (tp30) REVERT: G 149 MET cc_start: 0.9218 (tpp) cc_final: 0.8987 (mmm) REVERT: I 199 ASN cc_start: 0.8981 (OUTLIER) cc_final: 0.8753 (p0) REVERT: I 292 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8863 (mm) REVERT: J 95 ASP cc_start: 0.8947 (t0) cc_final: 0.8220 (m-30) outliers start: 57 outliers final: 29 residues processed: 162 average time/residue: 0.3526 time to fit residues: 93.1268 Evaluate side-chains 131 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 148 CYS 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 179 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain L residue 78 LEU 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 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 F residue 73 LEU Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 163 ASN Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 317 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 151 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 190 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 130 optimal weight: 0.0170 chunk 179 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN ** G 169 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 = 0.3152 r_free = 0.3152 target = 0.043857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.032919 restraints weight = 114146.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.034115 restraints weight = 61561.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.034924 restraints weight = 42128.253| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18000 Z= 0.133 Angle : 0.611 10.980 24474 Z= 0.301 Chirality : 0.042 0.243 2706 Planarity : 0.005 0.140 3117 Dihedral : 6.588 59.470 2990 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.52 % Favored : 94.34 % Rotamer: Outliers : 3.82 % Allowed : 23.05 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.18), residues: 2157 helix: 1.77 (0.27), residues: 369 sheet: 0.04 (0.25), residues: 429 loop : -1.34 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 153 HIS 0.004 0.001 HIS C 25 PHE 0.013 0.001 PHE E 67 TYR 0.020 0.001 TYR D 98 ARG 0.006 0.000 ARG H 13 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 24) link_NAG-ASN : angle 1.91420 ( 72) link_BETA1-4 : bond 0.00553 ( 6) link_BETA1-4 : angle 1.83617 ( 18) hydrogen bonds : bond 0.04122 ( 512) hydrogen bonds : angle 5.40143 ( 1455) SS BOND : bond 0.00310 ( 27) SS BOND : angle 1.71033 ( 54) covalent geometry : bond 0.00297 (17943) covalent geometry : angle 0.59650 (24330) *********************** 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 172 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 100 time to evaluate : 2.212 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: 0.8110 (OUTLIER) cc_final: 0.7703 (tt) REVERT: B 77 MET cc_start: 0.8605 (mpp) cc_final: 0.8068 (mmt) REVERT: B 149 MET cc_start: 0.9172 (tpp) cc_final: 0.8870 (mmm) REVERT: A 24 ASP cc_start: 0.9382 (m-30) cc_final: 0.9145 (t0) REVERT: A 225 ASP cc_start: 0.8805 (t70) cc_final: 0.8500 (t0) REVERT: A 278 ASP cc_start: 0.9100 (t0) cc_final: 0.8823 (t0) REVERT: H 13 ARG cc_start: 0.8928 (mtt-85) cc_final: 0.8202 (mtt-85) REVERT: H 95 ASP cc_start: 0.8958 (t0) cc_final: 0.8355 (m-30) REVERT: L 32 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8509 (mt-10) REVERT: C 14 TRP cc_start: 0.9220 (OUTLIER) cc_final: 0.8977 (m-90) REVERT: C 147 GLU cc_start: 0.9415 (OUTLIER) cc_final: 0.9197 (tp30) REVERT: C 149 MET cc_start: 0.9202 (tpp) cc_final: 0.8785 (tpp) REVERT: D 278 ASP cc_start: 0.9051 (t0) cc_final: 0.8809 (t0) REVERT: E 72 ASP cc_start: 0.8052 (t70) cc_final: 0.7578 (t70) REVERT: E 75 GLN cc_start: 0.9488 (mt0) cc_final: 0.9149 (mt0) REVERT: E 95 ASP cc_start: 0.8878 (t0) cc_final: 0.8282 (m-30) REVERT: F 82 ASP cc_start: 0.8188 (m-30) cc_final: 0.7845 (m-30) REVERT: G 77 MET cc_start: 0.8572 (mmt) cc_final: 0.8028 (mmt) REVERT: G 149 MET cc_start: 0.9237 (tpp) cc_final: 0.8943 (tpp) REVERT: I 199 ASN cc_start: 0.9010 (OUTLIER) cc_final: 0.8789 (p0) REVERT: I 292 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8832 (mm) REVERT: J 95 ASP cc_start: 0.8997 (t0) cc_final: 0.8209 (m-30) REVERT: K 73 LEU cc_start: 0.8891 (tp) cc_final: 0.8655 (tp) outliers start: 72 outliers final: 53 residues processed: 164 average time/residue: 0.3124 time to fit residues: 82.4036 Evaluate side-chains 150 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 92 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 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 56 ILE Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 123 ILE 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 269 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain H residue 2 VAL 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 108 LEU Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 30 CYS Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 102 THR 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 163 ASN Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 208 HIS 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 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 107 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 203 optimal weight: 2.9990 chunk 138 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.042030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.031379 restraints weight = 113669.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.032512 restraints weight = 62877.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.033288 restraints weight = 43816.093| |-----------------------------------------------------------------------------| r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18000 Z= 0.236 Angle : 0.683 9.593 24474 Z= 0.342 Chirality : 0.043 0.254 2706 Planarity : 0.006 0.140 3117 Dihedral : 6.875 58.348 2990 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.77 % Favored : 93.09 % Rotamer: Outliers : 4.40 % Allowed : 23.48 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.18), residues: 2157 helix: 1.72 (0.27), residues: 372 sheet: -0.21 (0.25), residues: 453 loop : -1.34 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 153 HIS 0.006 0.001 HIS B 142 PHE 0.014 0.002 PHE A 213 TYR 0.013 0.002 TYR I 168 ARG 0.004 0.001 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 24) link_NAG-ASN : angle 2.04274 ( 72) link_BETA1-4 : bond 0.00422 ( 6) link_BETA1-4 : angle 1.48782 ( 18) hydrogen bonds : bond 0.04234 ( 512) hydrogen bonds : angle 5.56559 ( 1455) SS BOND : bond 0.00326 ( 27) SS BOND : angle 2.32563 ( 54) covalent geometry : bond 0.00517 (17943) covalent geometry : angle 0.66624 (24330) *********************** 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 178 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 95 time to evaluate : 2.126 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: 0.8135 (OUTLIER) cc_final: 0.7688 (tt) REVERT: B 77 MET cc_start: 0.8624 (mpp) cc_final: 0.8108 (mmt) REVERT: B 149 MET cc_start: 0.9136 (tpp) cc_final: 0.8917 (mmm) REVERT: A 53 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7226 (tt) REVERT: A 225 ASP cc_start: 0.8779 (t70) cc_final: 0.8491 (t0) REVERT: H 13 ARG cc_start: 0.8977 (mtt-85) cc_final: 0.8270 (mtt-85) REVERT: H 95 ASP cc_start: 0.9018 (t0) cc_final: 0.8639 (t70) REVERT: L 32 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8601 (mt-10) REVERT: C 149 MET cc_start: 0.9208 (tpp) cc_final: 0.8822 (tpp) REVERT: D 292 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9123 (mm) REVERT: E 95 ASP cc_start: 0.8905 (t0) cc_final: 0.8369 (m-30) REVERT: F 32 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8544 (mt-10) REVERT: F 82 ASP cc_start: 0.8182 (m-30) cc_final: 0.7855 (m-30) REVERT: G 147 GLU cc_start: 0.9430 (OUTLIER) cc_final: 0.9163 (tp30) REVERT: G 149 MET cc_start: 0.9226 (tpp) cc_final: 0.8877 (tpp) REVERT: I 199 ASN cc_start: 0.8998 (OUTLIER) cc_final: 0.8772 (p0) REVERT: J 95 ASP cc_start: 0.9002 (t0) cc_final: 0.8237 (m-30) REVERT: K 6 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.6853 (pt0) outliers start: 83 outliers final: 68 residues processed: 166 average time/residue: 0.3320 time to fit residues: 88.6010 Evaluate side-chains 164 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 90 time to evaluate : 2.961 ------------------------------------------------------------------------------- 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 53 LEU 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 136 SER Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 1 GLU 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 19 ASP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 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 104 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain E residue 68 THR 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 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 208 HIS Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain K residue 6 GLN 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 142 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 103 optimal weight: 0.1980 chunk 38 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 197 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** 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 = 0.3069 r_free = 0.3069 target = 0.041195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.030593 restraints weight = 118570.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.031669 restraints weight = 67152.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.032400 restraints weight = 47383.046| |-----------------------------------------------------------------------------| r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 18000 Z= 0.250 Angle : 0.697 10.977 24474 Z= 0.349 Chirality : 0.044 0.264 2706 Planarity : 0.006 0.137 3117 Dihedral : 6.964 55.765 2990 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.77 % Favored : 93.09 % Rotamer: Outliers : 5.19 % Allowed : 23.16 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.18), residues: 2157 helix: 1.73 (0.27), residues: 372 sheet: -0.45 (0.25), residues: 438 loop : -1.39 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 153 HIS 0.005 0.001 HIS B 142 PHE 0.014 0.002 PHE A 213 TYR 0.013 0.002 TYR A 168 ARG 0.010 0.001 ARG G 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 24) link_NAG-ASN : angle 2.06527 ( 72) link_BETA1-4 : bond 0.00304 ( 6) link_BETA1-4 : angle 1.37667 ( 18) hydrogen bonds : bond 0.04227 ( 512) hydrogen bonds : angle 5.54756 ( 1455) SS BOND : bond 0.00399 ( 27) SS BOND : angle 2.21404 ( 54) covalent geometry : bond 0.00543 (17943) covalent geometry : angle 0.68060 (24330) *********************** 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 190 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 92 time to evaluate : 2.403 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: 0.8138 (OUTLIER) cc_final: 0.7702 (tt) REVERT: B 77 MET cc_start: 0.8638 (mpp) cc_final: 0.8197 (mmt) REVERT: B 149 MET cc_start: 0.9151 (tpp) cc_final: 0.8906 (mmm) REVERT: H 95 ASP cc_start: 0.9023 (t0) cc_final: 0.8667 (t70) REVERT: L 32 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8587 (mt-10) REVERT: C 149 MET cc_start: 0.9179 (tpp) cc_final: 0.8803 (tpp) REVERT: D 292 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9184 (mm) REVERT: E 95 ASP cc_start: 0.8887 (t0) cc_final: 0.8371 (m-30) REVERT: F 6 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7859 (mt0) REVERT: F 32 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8487 (mt-10) REVERT: F 82 ASP cc_start: 0.8225 (m-30) cc_final: 0.7908 (m-30) REVERT: G 149 MET cc_start: 0.9219 (tpp) cc_final: 0.8881 (tpp) REVERT: I 199 ASN cc_start: 0.8945 (OUTLIER) cc_final: 0.8714 (p0) REVERT: I 292 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9000 (mm) REVERT: J 95 ASP cc_start: 0.8975 (t0) cc_final: 0.8239 (m-30) REVERT: K 6 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7317 (pt0) REVERT: K 32 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8344 (mt-10) outliers start: 98 outliers final: 76 residues processed: 177 average time/residue: 0.3259 time to fit residues: 93.2622 Evaluate side-chains 168 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 86 time to evaluate : 2.458 ------------------------------------------------------------------------------- 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 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 317 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 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 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 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 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 98 ASP Chi-restraints excluded: chain F residue 6 GLN 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 148 CYS Chi-restraints excluded: chain G residue 169 ASN Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 52 CYS 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 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 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 J residue 82 ASN 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 32 optimal weight: 3.9990 chunk 30 optimal weight: 0.0770 chunk 82 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 152 optimal weight: 0.9980 chunk 208 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 overall best weight: 3.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN G 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.041320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.030773 restraints weight = 118530.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.031899 restraints weight = 65504.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.032650 restraints weight = 45358.705| |-----------------------------------------------------------------------------| r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18000 Z= 0.191 Angle : 0.670 9.911 24474 Z= 0.335 Chirality : 0.043 0.252 2706 Planarity : 0.005 0.136 3117 Dihedral : 6.804 59.770 2988 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.98 % Favored : 93.88 % Rotamer: Outliers : 4.40 % Allowed : 24.27 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.18), residues: 2157 helix: 1.83 (0.27), residues: 372 sheet: -0.38 (0.24), residues: 456 loop : -1.37 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 153 HIS 0.005 0.001 HIS B 142 PHE 0.012 0.001 PHE D 118 TYR 0.017 0.001 TYR K 86 ARG 0.008 0.001 ARG H 13 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 24) link_NAG-ASN : angle 1.98018 ( 72) link_BETA1-4 : bond 0.00435 ( 6) link_BETA1-4 : angle 1.47987 ( 18) hydrogen bonds : bond 0.04057 ( 512) hydrogen bonds : angle 5.47012 ( 1455) SS BOND : bond 0.00484 ( 27) SS BOND : angle 1.91234 ( 54) covalent geometry : bond 0.00421 (17943) covalent geometry : angle 0.65628 (24330) *********************** 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 174 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 91 time to evaluate : 2.246 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: 0.8131 (OUTLIER) cc_final: 0.7692 (tt) REVERT: B 77 MET cc_start: 0.8552 (mpp) cc_final: 0.8129 (mmt) REVERT: B 149 MET cc_start: 0.9178 (tpp) cc_final: 0.8913 (mmm) REVERT: H 18 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7656 (mp) REVERT: H 95 ASP cc_start: 0.8989 (t0) cc_final: 0.8398 (m-30) REVERT: L 32 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8565 (mt-10) REVERT: C 14 TRP cc_start: 0.9299 (OUTLIER) cc_final: 0.8978 (m-90) REVERT: C 149 MET cc_start: 0.9218 (tpp) cc_final: 0.8869 (tpp) REVERT: D 292 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9129 (mm) REVERT: E 95 ASP cc_start: 0.8941 (t0) cc_final: 0.8403 (m-30) REVERT: F 32 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8445 (mt-10) REVERT: F 82 ASP cc_start: 0.8206 (m-30) cc_final: 0.7865 (m-30) REVERT: G 149 MET cc_start: 0.9234 (tpp) cc_final: 0.8990 (mmm) REVERT: I 199 ASN cc_start: 0.8929 (OUTLIER) cc_final: 0.8708 (p0) REVERT: I 292 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8991 (mm) REVERT: J 95 ASP cc_start: 0.8999 (t0) cc_final: 0.8209 (m-30) REVERT: K 32 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8298 (mt-10) REVERT: K 86 TYR cc_start: 0.8400 (m-10) cc_final: 0.8188 (m-10) outliers start: 83 outliers final: 73 residues processed: 167 average time/residue: 0.3491 time to fit residues: 94.1431 Evaluate side-chains 162 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 83 time to evaluate : 2.870 ------------------------------------------------------------------------------- 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 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 199 ASN 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 277 CYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain C residue 14 TRP Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 85 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 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 206 SER Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 277 CYS Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 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 98 ASP 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 I residue 12 THR Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 52 CYS 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 163 ASN Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 208 HIS Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 82 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 67 optimal weight: 0.4980 chunk 146 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 70 optimal weight: 0.0470 chunk 178 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 168 optimal weight: 0.9990 chunk 122 optimal weight: 0.0970 chunk 157 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** G 43 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 = 0.3108 r_free = 0.3108 target = 0.042216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.031678 restraints weight = 117510.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.032835 restraints weight = 64039.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.033616 restraints weight = 44003.574| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18000 Z= 0.115 Angle : 0.643 11.254 24474 Z= 0.316 Chirality : 0.043 0.250 2706 Planarity : 0.005 0.134 3117 Dihedral : 6.426 55.641 2988 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.91 % Favored : 94.95 % Rotamer: Outliers : 3.66 % Allowed : 24.70 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.18), residues: 2157 helix: 1.87 (0.27), residues: 372 sheet: -0.23 (0.24), residues: 471 loop : -1.32 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 14 HIS 0.004 0.001 HIS G 142 PHE 0.011 0.001 PHE D 118 TYR 0.014 0.001 TYR L 86 ARG 0.008 0.000 ARG H 13 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 24) link_NAG-ASN : angle 1.84252 ( 72) link_BETA1-4 : bond 0.00541 ( 6) link_BETA1-4 : angle 1.68796 ( 18) hydrogen bonds : bond 0.03905 ( 512) hydrogen bonds : angle 5.18192 ( 1455) SS BOND : bond 0.00281 ( 27) SS BOND : angle 1.60052 ( 54) covalent geometry : bond 0.00259 (17943) covalent geometry : angle 0.63049 (24330) *********************** 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 160 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 91 time to evaluate : 2.050 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: 0.8122 (OUTLIER) cc_final: 0.7700 (tt) REVERT: B 77 MET cc_start: 0.8486 (mpp) cc_final: 0.8082 (mmt) REVERT: B 149 MET cc_start: 0.9225 (tpp) cc_final: 0.8929 (mmm) REVERT: H 95 ASP cc_start: 0.8955 (t0) cc_final: 0.8363 (m-30) REVERT: L 4 MET cc_start: 0.8041 (mmm) cc_final: 0.7741 (mmm) REVERT: L 32 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8512 (mt-10) REVERT: L 82 ASP cc_start: 0.8035 (m-30) cc_final: 0.7707 (m-30) REVERT: C 14 TRP cc_start: 0.9224 (OUTLIER) cc_final: 0.8992 (m-90) REVERT: C 149 MET cc_start: 0.9209 (tpp) cc_final: 0.8691 (tpp) REVERT: D 225 ASP cc_start: 0.8731 (t0) cc_final: 0.8461 (t0) REVERT: D 283 THR cc_start: 0.9505 (OUTLIER) cc_final: 0.9236 (p) REVERT: D 292 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.8718 (mm) REVERT: E 95 ASP cc_start: 0.8924 (t0) cc_final: 0.8455 (m-30) REVERT: F 6 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7851 (mt0) REVERT: F 82 ASP cc_start: 0.8177 (m-30) cc_final: 0.7824 (m-30) REVERT: G 149 MET cc_start: 0.9252 (tpp) cc_final: 0.9006 (mmm) REVERT: I 199 ASN cc_start: 0.8961 (OUTLIER) cc_final: 0.8744 (p0) REVERT: I 292 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9013 (mm) REVERT: J 95 ASP cc_start: 0.8943 (t0) cc_final: 0.8609 (t70) REVERT: K 86 TYR cc_start: 0.8423 (m-10) cc_final: 0.8095 (m-10) outliers start: 69 outliers final: 54 residues processed: 155 average time/residue: 0.2804 time to fit residues: 70.7317 Evaluate side-chains 146 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 85 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 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 179 LEU Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain H residue 107 ILE 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 85 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain D residue 18 HIS 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 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 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 18 HIS Chi-restraints excluded: chain I residue 52 CYS 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 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 283 THR Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain J residue 82 ASN 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 27 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 117 optimal weight: 0.6980 chunk 151 optimal weight: 0.8980 chunk 192 optimal weight: 10.0000 chunk 201 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 41 optimal weight: 0.2980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.042975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.031865 restraints weight = 113639.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.033047 restraints weight = 61928.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.033842 restraints weight = 42922.102| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 18000 Z= 0.114 Angle : 0.648 11.492 24474 Z= 0.318 Chirality : 0.043 0.243 2706 Planarity : 0.005 0.133 3117 Dihedral : 6.279 55.637 2988 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.87 % Favored : 94.99 % Rotamer: Outliers : 3.23 % Allowed : 24.70 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.18), residues: 2157 helix: 1.85 (0.26), residues: 372 sheet: 0.13 (0.25), residues: 441 loop : -1.41 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 100E HIS 0.004 0.001 HIS C 25 PHE 0.011 0.001 PHE C 140 TYR 0.017 0.001 TYR L 86 ARG 0.009 0.000 ARG H 13 Details of bonding type rmsd link_NAG-ASN : bond 0.00207 ( 24) link_NAG-ASN : angle 1.83021 ( 72) link_BETA1-4 : bond 0.00529 ( 6) link_BETA1-4 : angle 1.75190 ( 18) hydrogen bonds : bond 0.03774 ( 512) hydrogen bonds : angle 5.27094 ( 1455) SS BOND : bond 0.00265 ( 27) SS BOND : angle 2.07778 ( 54) covalent geometry : bond 0.00261 (17943) covalent geometry : angle 0.63259 (24330) ********************** 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 154 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 93 time to evaluate : 2.188 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: 0.8124 (OUTLIER) cc_final: 0.7696 (tt) REVERT: B 77 MET cc_start: 0.8443 (mpp) cc_final: 0.8008 (mmt) REVERT: B 149 MET cc_start: 0.9236 (tpp) cc_final: 0.8928 (mmm) REVERT: H 95 ASP cc_start: 0.8937 (t0) cc_final: 0.8335 (m-30) REVERT: L 4 MET cc_start: 0.8104 (mmm) cc_final: 0.7798 (mmm) REVERT: L 32 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8488 (mt-10) REVERT: L 82 ASP cc_start: 0.7964 (m-30) cc_final: 0.7630 (m-30) REVERT: C 149 MET cc_start: 0.9188 (tpp) cc_final: 0.8834 (tpp) REVERT: D 225 ASP cc_start: 0.8793 (t0) cc_final: 0.8495 (t0) REVERT: D 283 THR cc_start: 0.9530 (OUTLIER) cc_final: 0.9250 (p) REVERT: E 1 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7790 (tm-30) REVERT: E 95 ASP cc_start: 0.8929 (t0) cc_final: 0.8453 (m-30) REVERT: F 6 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7839 (mt0) REVERT: F 82 ASP cc_start: 0.8166 (m-30) cc_final: 0.7846 (m-30) REVERT: G 149 MET cc_start: 0.9262 (tpp) cc_final: 0.9007 (mmm) REVERT: I 199 ASN cc_start: 0.8996 (OUTLIER) cc_final: 0.8788 (p0) REVERT: I 292 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8968 (mm) REVERT: J 95 ASP cc_start: 0.8937 (t0) cc_final: 0.8580 (t70) outliers start: 61 outliers final: 51 residues processed: 148 average time/residue: 0.2851 time to fit residues: 69.5827 Evaluate side-chains 143 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 87 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 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 179 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain D residue 18 HIS 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 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 98 ASP Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 78 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 52 CYS 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 183 HIS Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 214 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 K residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 88 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 193 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 97 optimal weight: 0.1980 chunk 114 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.042292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.031601 restraints weight = 113868.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.032750 restraints weight = 62283.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.033521 restraints weight = 42920.199| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18000 Z= 0.153 Angle : 0.640 10.773 24474 Z= 0.317 Chirality : 0.043 0.244 2706 Planarity : 0.005 0.135 3117 Dihedral : 6.196 55.711 2988 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.52 % Favored : 94.34 % Rotamer: Outliers : 3.50 % Allowed : 24.54 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.18), residues: 2157 helix: 1.95 (0.26), residues: 372 sheet: -0.20 (0.24), residues: 471 loop : -1.33 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP C 14 HIS 0.009 0.001 HIS I 184 PHE 0.010 0.001 PHE D 118 TYR 0.023 0.001 TYR L 86 ARG 0.009 0.000 ARG H 13 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 24) link_NAG-ASN : angle 1.90950 ( 72) link_BETA1-4 : bond 0.00489 ( 6) link_BETA1-4 : angle 1.60488 ( 18) hydrogen bonds : bond 0.03778 ( 512) hydrogen bonds : angle 5.16767 ( 1455) SS BOND : bond 0.00367 ( 27) SS BOND : angle 1.44369 ( 54) covalent geometry : bond 0.00343 (17943) covalent geometry : angle 0.62783 (24330) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5778.52 seconds wall clock time: 107 minutes 56.81 seconds (6476.81 seconds total)