Starting phenix.real_space_refine on Sun Aug 24 09:24:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xn4_38497/08_2025/8xn4_38497.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xn4_38497/08_2025/8xn4_38497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xn4_38497/08_2025/8xn4_38497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xn4_38497/08_2025/8xn4_38497.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xn4_38497/08_2025/8xn4_38497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xn4_38497/08_2025/8xn4_38497.map" } resolution = 2.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.080 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 112 5.16 5 C 12026 2.51 5 N 3269 2.21 5 O 3766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 145 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19173 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1393 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "B" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1393 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "C" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1393 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "D" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1393 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "E" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1393 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "F" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1393 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "G" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1393 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "H" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "I" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "J" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "K" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "L" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "M" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "N" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Time building chain proxies: 4.18, per 1000 atoms: 0.22 Number of scatterers: 19173 At special positions: 0 Unit cell: (115.92, 115.92, 108.36, 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 112 16.00 O 3766 8.00 N 3269 7.00 C 12026 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 798.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4676 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 41 sheets defined 53.3% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 31 through 44 Processing helix chain 'A' and resid 53 through 68 Processing helix chain 'A' and resid 85 through 99 Processing helix chain 'A' and resid 113 through 120 removed outlier: 3.719A pdb=" N PHE A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 174 removed outlier: 3.637A pdb=" N LYS A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 185 Processing helix chain 'A' and resid 191 through 199 Processing helix chain 'B' and resid 32 through 42 Processing helix chain 'B' and resid 53 through 68 Processing helix chain 'B' and resid 85 through 99 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 148 through 174 Processing helix chain 'B' and resid 176 through 184 Processing helix chain 'B' and resid 191 through 199 Processing helix chain 'C' and resid 32 through 43 Processing helix chain 'C' and resid 53 through 68 Processing helix chain 'C' and resid 85 through 99 Processing helix chain 'C' and resid 113 through 120 Processing helix chain 'C' and resid 149 through 174 removed outlier: 3.572A pdb=" N ILE C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 191 through 199 Processing helix chain 'D' and resid 34 through 43 Processing helix chain 'D' and resid 53 through 68 Processing helix chain 'D' and resid 85 through 99 Processing helix chain 'D' and resid 113 through 120 Processing helix chain 'D' and resid 148 through 174 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 191 through 199 Processing helix chain 'D' and resid 207 through 211 removed outlier: 3.515A pdb=" N MET D 211 " --> pdb=" O ALA D 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 42 Processing helix chain 'E' and resid 53 through 68 Processing helix chain 'E' and resid 85 through 99 removed outlier: 3.678A pdb=" N GLY E 89 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 121 removed outlier: 3.738A pdb=" N PHE E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 174 Processing helix chain 'E' and resid 176 through 185 removed outlier: 3.528A pdb=" N ILE E 180 " --> pdb=" O THR E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 199 Processing helix chain 'F' and resid 32 through 42 Processing helix chain 'F' and resid 53 through 68 Processing helix chain 'F' and resid 85 through 99 Processing helix chain 'F' and resid 113 through 121 removed outlier: 3.652A pdb=" N PHE F 117 " --> pdb=" O ALA F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 174 Processing helix chain 'F' and resid 176 through 184 Processing helix chain 'F' and resid 191 through 199 Processing helix chain 'F' and resid 207 through 211 removed outlier: 3.595A pdb=" N MET F 211 " --> pdb=" O ALA F 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 42 Processing helix chain 'G' and resid 53 through 68 Processing helix chain 'G' and resid 85 through 99 removed outlier: 3.606A pdb=" N GLY G 89 " --> pdb=" O SER G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 120 removed outlier: 3.709A pdb=" N PHE G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 174 Processing helix chain 'G' and resid 176 through 184 Processing helix chain 'G' and resid 191 through 199 Processing helix chain 'H' and resid 53 through 60 Processing helix chain 'H' and resid 70 through 87 removed outlier: 3.557A pdb=" N MET H 87 " --> pdb=" O CYS H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 117 removed outlier: 3.503A pdb=" N LEU H 107 " --> pdb=" O SER H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 138 Processing helix chain 'H' and resid 167 through 191 Processing helix chain 'H' and resid 195 through 203 Processing helix chain 'H' and resid 210 through 218 Processing helix chain 'I' and resid 53 through 60 Processing helix chain 'I' and resid 70 through 87 Processing helix chain 'I' and resid 103 through 117 Processing helix chain 'I' and resid 131 through 138 Processing helix chain 'I' and resid 167 through 192 Processing helix chain 'I' and resid 195 through 203 Processing helix chain 'I' and resid 210 through 218 Processing helix chain 'J' and resid 53 through 59 Processing helix chain 'J' and resid 70 through 87 removed outlier: 3.546A pdb=" N MET J 87 " --> pdb=" O CYS J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 117 Processing helix chain 'J' and resid 130 through 138 Processing helix chain 'J' and resid 167 through 193 Processing helix chain 'J' and resid 195 through 202 Processing helix chain 'J' and resid 210 through 218 Processing helix chain 'K' and resid 53 through 60 Processing helix chain 'K' and resid 70 through 88 removed outlier: 3.819A pdb=" N MET K 87 " --> pdb=" O CYS K 83 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP K 88 " --> pdb=" O LEU K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 117 Processing helix chain 'K' and resid 131 through 138 Processing helix chain 'K' and resid 167 through 191 Processing helix chain 'K' and resid 195 through 204 Processing helix chain 'K' and resid 210 through 218 Processing helix chain 'L' and resid 53 through 60 Processing helix chain 'L' and resid 70 through 87 Processing helix chain 'L' and resid 103 through 117 Processing helix chain 'L' and resid 130 through 138 Processing helix chain 'L' and resid 166 through 191 removed outlier: 3.642A pdb=" N LEU L 170 " --> pdb=" O GLN L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 203 Processing helix chain 'L' and resid 210 through 218 Processing helix chain 'M' and resid 53 through 60 removed outlier: 3.502A pdb=" N GLU M 60 " --> pdb=" O LYS M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 87 Processing helix chain 'M' and resid 103 through 117 removed outlier: 3.540A pdb=" N LEU M 107 " --> pdb=" O SER M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 138 Processing helix chain 'M' and resid 167 through 192 Processing helix chain 'M' and resid 195 through 204 removed outlier: 3.535A pdb=" N GLU M 204 " --> pdb=" O ARG M 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 218 Processing helix chain 'N' and resid 53 through 60 Processing helix chain 'N' and resid 70 through 87 removed outlier: 3.736A pdb=" N MET N 87 " --> pdb=" O CYS N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 117 Processing helix chain 'N' and resid 131 through 138 Processing helix chain 'N' and resid 167 through 192 Processing helix chain 'N' and resid 195 through 204 removed outlier: 3.601A pdb=" N GLU N 204 " --> pdb=" O ARG N 200 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 218 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 48 removed outlier: 7.031A pdb=" N ILE A 46 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ASN A 80 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 48 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A 75 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE A 106 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 77 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N MET A 108 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE A 79 " --> pdb=" O MET A 108 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU A 110 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU A 134 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLY A 109 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LEU A 136 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA A 111 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 188 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 48 removed outlier: 7.031A pdb=" N ILE A 46 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ASN A 80 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 48 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A 75 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE A 106 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 77 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N MET A 108 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE A 79 " --> pdb=" O MET A 108 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU A 110 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N PHE A 128 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR A 105 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 142 Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 48 removed outlier: 5.476A pdb=" N SER B 81 " --> pdb=" O MET B 108 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU B 110 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU B 134 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY B 109 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU B 136 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA B 111 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 188 " --> pdb=" O ILE B 137 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 45 through 48 removed outlier: 5.476A pdb=" N SER B 81 " --> pdb=" O MET B 108 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU B 110 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N PHE B 128 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N THR B 105 " --> pdb=" O PHE B 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.559A pdb=" N ALA B 142 " --> pdb=" O GLY J 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY J 165 " --> pdb=" O ALA B 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.717A pdb=" N ILE C 46 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ASN C 80 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU C 48 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE C 75 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE C 106 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU C 77 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N MET C 108 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE C 79 " --> pdb=" O MET C 108 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU C 110 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.717A pdb=" N ILE C 46 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ASN C 80 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU C 48 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE C 75 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE C 106 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU C 77 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N MET C 108 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE C 79 " --> pdb=" O MET C 108 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU C 110 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N PHE C 128 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N THR C 105 " --> pdb=" O PHE C 128 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.525A pdb=" N GLY K 165 " --> pdb=" O ALA C 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 146 through 147 Processing sheet with id=AB4, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.713A pdb=" N ILE D 46 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ASN D 80 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU D 48 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE D 75 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE D 106 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU D 77 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N MET D 108 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ILE D 79 " --> pdb=" O MET D 108 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LEU D 110 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU D 134 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY D 109 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU D 136 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA D 111 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.713A pdb=" N ILE D 46 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ASN D 80 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU D 48 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE D 75 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE D 106 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU D 77 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N MET D 108 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ILE D 79 " --> pdb=" O MET D 108 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LEU D 110 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE D 128 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N THR D 105 " --> pdb=" O PHE D 128 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 146 through 147 Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 48 removed outlier: 6.367A pdb=" N ILE E 75 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE E 106 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU E 77 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N MET E 108 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE E 79 " --> pdb=" O MET E 108 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU E 110 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLU E 134 " --> pdb=" O ALA E 107 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY E 109 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N LEU E 136 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA E 111 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 48 removed outlier: 6.367A pdb=" N ILE E 75 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE E 106 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU E 77 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N MET E 108 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE E 79 " --> pdb=" O MET E 108 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU E 110 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N PHE E 128 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR E 105 " --> pdb=" O PHE E 128 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 141 through 142 removed outlier: 3.507A pdb=" N ALA E 142 " --> pdb=" O GLY M 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY M 165 " --> pdb=" O ALA E 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 146 through 147 Processing sheet with id=AC2, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.469A pdb=" N ILE F 75 " --> pdb=" O VAL F 104 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ILE F 106 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU F 77 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N MET F 108 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE F 79 " --> pdb=" O MET F 108 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LEU F 110 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLU F 134 " --> pdb=" O ALA F 107 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY F 109 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU F 136 " --> pdb=" O GLY F 109 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA F 111 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG F 188 " --> pdb=" O ILE F 137 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.469A pdb=" N ILE F 75 " --> pdb=" O VAL F 104 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ILE F 106 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU F 77 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N MET F 108 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE F 79 " --> pdb=" O MET F 108 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LEU F 110 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N PHE F 128 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR F 105 " --> pdb=" O PHE F 128 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 141 through 142 Processing sheet with id=AC5, first strand: chain 'F' and resid 146 through 147 Processing sheet with id=AC6, first strand: chain 'G' and resid 45 through 48 removed outlier: 6.695A pdb=" N ILE G 46 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASN G 80 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU G 48 " --> pdb=" O ASN G 80 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N SER G 81 " --> pdb=" O MET G 108 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU G 110 " --> pdb=" O SER G 81 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 45 through 48 removed outlier: 6.695A pdb=" N ILE G 46 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASN G 80 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU G 48 " --> pdb=" O ASN G 80 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N SER G 81 " --> pdb=" O MET G 108 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU G 110 " --> pdb=" O SER G 81 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N PHE G 128 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR G 105 " --> pdb=" O PHE G 128 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 141 through 142 Processing sheet with id=AC9, first strand: chain 'G' and resid 146 through 147 Processing sheet with id=AD1, first strand: chain 'H' and resid 62 through 65 removed outlier: 6.423A pdb=" N ILE H 93 " --> pdb=" O GLN H 122 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL H 124 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL H 95 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N MET H 126 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE H 97 " --> pdb=" O MET H 126 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLN H 128 " --> pdb=" O ILE H 97 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER H 99 " --> pdb=" O GLN H 128 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ARG H 152 " --> pdb=" O CYS H 125 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLY H 127 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N LEU H 154 " --> pdb=" O GLY H 127 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA H 129 " --> pdb=" O LEU H 154 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 62 through 65 removed outlier: 6.423A pdb=" N ILE H 93 " --> pdb=" O GLN H 122 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL H 124 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL H 95 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N MET H 126 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE H 97 " --> pdb=" O MET H 126 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLN H 128 " --> pdb=" O ILE H 97 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER H 99 " --> pdb=" O GLN H 128 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N MET H 146 " --> pdb=" O VAL H 121 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR H 123 " --> pdb=" O MET H 146 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 62 through 65 removed outlier: 5.465A pdb=" N SER I 99 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLN I 128 " --> pdb=" O SER I 99 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG I 152 " --> pdb=" O GLY I 127 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 62 through 65 removed outlier: 5.465A pdb=" N SER I 99 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLN I 128 " --> pdb=" O SER I 99 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N MET I 146 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N THR I 123 " --> pdb=" O MET I 146 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 62 through 65 removed outlier: 6.332A pdb=" N ILE J 93 " --> pdb=" O GLN J 122 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL J 124 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL J 95 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N MET J 126 " --> pdb=" O VAL J 95 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE J 97 " --> pdb=" O MET J 126 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN J 128 " --> pdb=" O ILE J 97 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ARG J 152 " --> pdb=" O CYS J 125 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLY J 127 " --> pdb=" O ARG J 152 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N LEU J 154 " --> pdb=" O GLY J 127 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA J 129 " --> pdb=" O LEU J 154 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 62 through 65 removed outlier: 6.332A pdb=" N ILE J 93 " --> pdb=" O GLN J 122 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL J 124 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL J 95 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N MET J 126 " --> pdb=" O VAL J 95 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE J 97 " --> pdb=" O MET J 126 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN J 128 " --> pdb=" O ILE J 97 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN J 222 " --> pdb=" O ARG J 145 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 62 through 65 removed outlier: 5.579A pdb=" N SER K 99 " --> pdb=" O MET K 126 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN K 128 " --> pdb=" O SER K 99 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG K 152 " --> pdb=" O GLY K 127 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 62 through 65 removed outlier: 5.579A pdb=" N SER K 99 " --> pdb=" O MET K 126 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN K 128 " --> pdb=" O SER K 99 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N MET K 146 " --> pdb=" O VAL K 121 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR K 123 " --> pdb=" O MET K 146 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 62 through 65 removed outlier: 6.187A pdb=" N ILE L 93 " --> pdb=" O GLN L 122 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL L 124 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL L 95 " --> pdb=" O VAL L 124 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N MET L 126 " --> pdb=" O VAL L 95 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE L 97 " --> pdb=" O MET L 126 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLN L 128 " --> pdb=" O ILE L 97 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ARG L 152 " --> pdb=" O CYS L 125 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY L 127 " --> pdb=" O ARG L 152 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N LEU L 154 " --> pdb=" O GLY L 127 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA L 129 " --> pdb=" O LEU L 154 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 62 through 65 removed outlier: 6.187A pdb=" N ILE L 93 " --> pdb=" O GLN L 122 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL L 124 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL L 95 " --> pdb=" O VAL L 124 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N MET L 126 " --> pdb=" O VAL L 95 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE L 97 " --> pdb=" O MET L 126 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLN L 128 " --> pdb=" O ILE L 97 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ARG L 145 " --> pdb=" O GLN L 222 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 62 through 65 removed outlier: 6.781A pdb=" N ILE M 63 " --> pdb=" O TYR M 96 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ASN M 98 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU M 65 " --> pdb=" O ASN M 98 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE M 93 " --> pdb=" O GLN M 122 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL M 124 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL M 95 " --> pdb=" O VAL M 124 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N MET M 126 " --> pdb=" O VAL M 95 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE M 97 " --> pdb=" O MET M 126 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLN M 128 " --> pdb=" O ILE M 97 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS M 207 " --> pdb=" O ILE M 155 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 62 through 65 removed outlier: 6.781A pdb=" N ILE M 63 " --> pdb=" O TYR M 96 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ASN M 98 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU M 65 " --> pdb=" O ASN M 98 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE M 93 " --> pdb=" O GLN M 122 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL M 124 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL M 95 " --> pdb=" O VAL M 124 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N MET M 126 " --> pdb=" O VAL M 95 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE M 97 " --> pdb=" O MET M 126 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLN M 128 " --> pdb=" O ILE M 97 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N MET M 146 " --> pdb=" O VAL M 121 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N THR M 123 " --> pdb=" O MET M 146 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 62 through 65 removed outlier: 6.846A pdb=" N ILE N 63 " --> pdb=" O TYR N 96 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASN N 98 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU N 65 " --> pdb=" O ASN N 98 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE N 93 " --> pdb=" O GLN N 122 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL N 124 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL N 95 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N MET N 126 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE N 97 " --> pdb=" O MET N 126 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN N 128 " --> pdb=" O ILE N 97 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 62 through 65 removed outlier: 6.846A pdb=" N ILE N 63 " --> pdb=" O TYR N 96 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASN N 98 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU N 65 " --> pdb=" O ASN N 98 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE N 93 " --> pdb=" O GLN N 122 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL N 124 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL N 95 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N MET N 126 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE N 97 " --> pdb=" O MET N 126 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN N 128 " --> pdb=" O ILE N 97 " (cutoff:3.500A) 1171 hydrogen bonds defined for protein. 3399 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.00 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 3387 1.30 - 1.43: 4415 1.43 - 1.56: 11448 1.56 - 1.69: 0 1.69 - 1.82: 210 Bond restraints: 19460 Sorted by residual: bond pdb=" CA SER L 160 " pdb=" CB SER L 160 " ideal model delta sigma weight residual 1.530 1.451 0.079 1.36e-02 5.41e+03 3.41e+01 bond pdb=" C ASP E 185 " pdb=" O ASP E 185 " ideal model delta sigma weight residual 1.235 1.165 0.070 1.26e-02 6.30e+03 3.13e+01 bond pdb=" C GLU E 178 " pdb=" O GLU E 178 " ideal model delta sigma weight residual 1.237 1.297 -0.061 1.16e-02 7.43e+03 2.75e+01 bond pdb=" C THR E 181 " pdb=" O THR E 181 " ideal model delta sigma weight residual 1.236 1.289 -0.053 1.16e-02 7.43e+03 2.06e+01 bond pdb=" C PRO J 119 " pdb=" O PRO J 119 " ideal model delta sigma weight residual 1.233 1.182 0.051 1.19e-02 7.06e+03 1.84e+01 ... (remaining 19455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 25890 2.72 - 5.44: 427 5.44 - 8.16: 34 8.16 - 10.88: 10 10.88 - 13.60: 8 Bond angle restraints: 26369 Sorted by residual: angle pdb=" C THR K 108 " pdb=" CA THR K 108 " pdb=" CB THR K 108 " ideal model delta sigma weight residual 109.95 122.12 -12.17 1.99e+00 2.53e-01 3.74e+01 angle pdb=" N THR K 108 " pdb=" CA THR K 108 " pdb=" C THR K 108 " ideal model delta sigma weight residual 113.18 106.02 7.16 1.21e+00 6.83e-01 3.50e+01 angle pdb=" C THR K 194 " pdb=" CA THR K 194 " pdb=" CB THR K 194 " ideal model delta sigma weight residual 108.86 117.06 -8.20 1.44e+00 4.82e-01 3.24e+01 angle pdb=" C THR J 194 " pdb=" CA THR J 194 " pdb=" CB THR J 194 " ideal model delta sigma weight residual 109.37 118.08 -8.71 1.59e+00 3.96e-01 3.00e+01 angle pdb=" C ALA C 113 " pdb=" CA ALA C 113 " pdb=" CB ALA C 113 " ideal model delta sigma weight residual 117.23 110.32 6.91 1.36e+00 5.41e-01 2.58e+01 ... (remaining 26364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 10202 17.98 - 35.97: 1240 35.97 - 53.95: 384 53.95 - 71.93: 84 71.93 - 89.91: 39 Dihedral angle restraints: 11949 sinusoidal: 4697 harmonic: 7252 Sorted by residual: dihedral pdb=" CA GLU A 43 " pdb=" C GLU A 43 " pdb=" N ARG A 44 " pdb=" CA ARG A 44 " ideal model delta harmonic sigma weight residual 180.00 152.61 27.39 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" C THR K 108 " pdb=" N THR K 108 " pdb=" CA THR K 108 " pdb=" CB THR K 108 " ideal model delta harmonic sigma weight residual -122.00 -134.51 12.51 0 2.50e+00 1.60e-01 2.50e+01 dihedral pdb=" CA MET J 87 " pdb=" C MET J 87 " pdb=" N ASP J 88 " pdb=" CA ASP J 88 " ideal model delta harmonic sigma weight residual -180.00 -158.31 -21.69 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 11946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2592 0.063 - 0.127: 430 0.127 - 0.190: 44 0.190 - 0.253: 5 0.253 - 0.317: 2 Chirality restraints: 3073 Sorted by residual: chirality pdb=" CB VAL N 117 " pdb=" CA VAL N 117 " pdb=" CG1 VAL N 117 " pdb=" CG2 VAL N 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA THR K 108 " pdb=" N THR K 108 " pdb=" C THR K 108 " pdb=" CB THR K 108 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA VAL N 117 " pdb=" N VAL N 117 " pdb=" C VAL N 117 " pdb=" CB VAL N 117 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 3070 not shown) Planarity restraints: 3451 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS K 191 " 0.022 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C HIS K 191 " -0.074 2.00e-02 2.50e+03 pdb=" O HIS K 191 " 0.026 2.00e-02 2.50e+03 pdb=" N SER K 192 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP F 70 " 0.061 5.00e-02 4.00e+02 9.55e-02 1.46e+01 pdb=" N PRO F 71 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO F 71 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO F 71 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 70 " 0.061 5.00e-02 4.00e+02 9.41e-02 1.42e+01 pdb=" N PRO D 71 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO D 71 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 71 " 0.050 5.00e-02 4.00e+02 ... (remaining 3448 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1829 2.74 - 3.28: 18769 3.28 - 3.82: 31384 3.82 - 4.36: 35858 4.36 - 4.90: 63556 Nonbonded interactions: 151396 Sorted by model distance: nonbonded pdb=" OE1 GLN L 222 " pdb=" N VAL L 223 " model vdw 2.200 3.120 nonbonded pdb=" OD2 ASP I 202 " pdb=" OH TYR I 217 " model vdw 2.205 3.040 nonbonded pdb=" O GLU L 171 " pdb=" ND2 ASN L 175 " model vdw 2.211 3.120 nonbonded pdb=" NH2 ARG A 186 " pdb=" OE2 GLU H 204 " model vdw 2.213 3.120 nonbonded pdb=" OH TYR N 159 " pdb=" OE2 GLU N 161 " model vdw 2.216 3.040 ... (remaining 151391 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.120 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 19460 Z= 0.277 Angle : 0.808 13.603 26369 Z= 0.466 Chirality : 0.047 0.317 3073 Planarity : 0.007 0.128 3451 Dihedral : 18.213 89.913 7273 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.46 % Favored : 97.42 % Rotamer: Outliers : 3.23 % Allowed : 31.46 % Favored : 65.31 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.17), residues: 2478 helix: 1.73 (0.15), residues: 1337 sheet: 1.73 (0.34), residues: 217 loop : -0.57 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 182 TYR 0.021 0.001 TYR C 98 PHE 0.023 0.002 PHE A 128 TRP 0.047 0.004 TRP A 189 HIS 0.006 0.001 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00476 (19460) covalent geometry : angle 0.80843 (26369) hydrogen bonds : bond 0.18790 ( 1103) hydrogen bonds : angle 5.82530 ( 3399) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 762 time to evaluate : 0.598 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: C 179 GLN cc_start: 0.8976 (tp40) cc_final: 0.8357 (tp-100) REVERT: C 182 ARG cc_start: 0.8494 (ttp80) cc_final: 0.7887 (ttp80) REVERT: H 85 GLU cc_start: 0.7597 (tp30) cc_final: 0.7379 (tp30) REVERT: H 202 ASP cc_start: 0.8425 (m-30) cc_final: 0.8213 (m-30) REVERT: I 126 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8669 (ptp) REVERT: J 152 ARG cc_start: 0.6289 (ptm160) cc_final: 0.5551 (ptm160) REVERT: K 104 PHE cc_start: 0.4428 (OUTLIER) cc_final: 0.3445 (m-80) REVERT: L 78 MET cc_start: 0.7914 (ptt) cc_final: 0.7707 (ptt) REVERT: M 91 ARG cc_start: 0.8919 (mtp85) cc_final: 0.8678 (mtp180) REVERT: M 152 ARG cc_start: 0.6330 (ptm160) cc_final: 0.5035 (ptm160) REVERT: N 117 VAL cc_start: 0.8814 (OUTLIER) cc_final: 0.8614 (m) outliers start: 66 outliers final: 35 residues processed: 795 average time/residue: 0.5456 time to fit residues: 485.3866 Evaluate side-chains 791 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 753 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain I residue 126 MET Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 168 SER Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 161 GLU Chi-restraints excluded: chain L residue 216 SER Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 122 GLN Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 223 VAL Chi-restraints excluded: chain N residue 225 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.0170 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 63 GLN A 171 GLN A 179 GLN B 58 ASN B 80 ASN B 171 GLN C 58 ASN D 58 ASN E 132 ASN E 138 HIS E 139 GLN F 35 GLN F 171 GLN F 179 GLN G 38 ASN G 58 ASN G 116 GLN H 75 ASN H 157 GLN I 75 ASN J 98 ASN K 75 ASN K 98 ASN K 122 GLN K 175 ASN L 75 ASN L 156 HIS M 75 ASN M 80 GLN N 75 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.112183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.102970 restraints weight = 28357.145| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.80 r_work: 0.3478 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19460 Z= 0.144 Angle : 0.600 9.737 26369 Z= 0.310 Chirality : 0.042 0.153 3073 Planarity : 0.005 0.067 3451 Dihedral : 6.276 77.766 2767 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 5.68 % Allowed : 25.34 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.17), residues: 2478 helix: 2.13 (0.15), residues: 1358 sheet: 1.77 (0.33), residues: 217 loop : -0.58 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 91 TYR 0.012 0.001 TYR I 159 PHE 0.010 0.001 PHE H 104 TRP 0.015 0.002 TRP A 189 HIS 0.005 0.001 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00341 (19460) covalent geometry : angle 0.59971 (26369) hydrogen bonds : bond 0.04636 ( 1103) hydrogen bonds : angle 4.06501 ( 3399) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 754 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7677 (tpt-90) REVERT: A 167 GLU cc_start: 0.8360 (tp30) cc_final: 0.8146 (tp30) REVERT: B 97 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8390 (mp10) REVERT: C 97 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8595 (mp10) REVERT: F 134 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8310 (tm-30) REVERT: H 59 GLU cc_start: 0.8242 (mp0) cc_final: 0.7996 (mp0) REVERT: H 85 GLU cc_start: 0.7661 (tp30) cc_final: 0.7434 (tp30) REVERT: H 124 VAL cc_start: 0.8815 (m) cc_final: 0.8607 (t) REVERT: I 181 ARG cc_start: 0.8555 (ttt90) cc_final: 0.8148 (ttt180) REVERT: J 104 PHE cc_start: 0.4424 (OUTLIER) cc_final: 0.4089 (m-80) REVERT: J 204 GLU cc_start: 0.8163 (tp30) cc_final: 0.7953 (tp30) REVERT: K 104 PHE cc_start: 0.4148 (OUTLIER) cc_final: 0.3285 (m-80) REVERT: L 59 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8256 (mm-30) REVERT: L 60 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: M 146 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8039 (mpt) REVERT: M 152 ARG cc_start: 0.6449 (ptm160) cc_final: 0.5114 (ptm160) REVERT: N 75 ASN cc_start: 0.8644 (m-40) cc_final: 0.8433 (m110) outliers start: 116 outliers final: 52 residues processed: 810 average time/residue: 0.5183 time to fit residues: 471.4056 Evaluate side-chains 808 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 748 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 116 GLN Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 128 GLN Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 225 SER Chi-restraints excluded: chain K residue 58 PHE Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 180 MET Chi-restraints excluded: chain K residue 200 ARG Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 161 GLU Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 216 SER Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 208 ILE Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 15 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 213 optimal weight: 0.9980 chunk 227 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 63 GLN A 80 ASN A 171 GLN A 179 GLN B 38 ASN B 58 ASN B 171 GLN B 179 GLN C 138 HIS C 139 GLN C 179 GLN D 58 ASN D 179 GLN E 58 ASN E 132 ASN E 138 HIS F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 50 GLN G 58 ASN G 132 ASN H 157 GLN I 75 ASN K 75 ASN K 98 ASN K 222 GLN L 75 ASN ** L 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 ASN M 75 ASN M 98 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.110876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.101606 restraints weight = 28067.445| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.79 r_work: 0.3445 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19460 Z= 0.185 Angle : 0.625 11.766 26369 Z= 0.320 Chirality : 0.043 0.157 3073 Planarity : 0.005 0.051 3451 Dihedral : 5.539 56.060 2728 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 5.92 % Allowed : 25.24 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.17), residues: 2478 helix: 2.16 (0.14), residues: 1358 sheet: 1.61 (0.33), residues: 217 loop : -0.62 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 181 TYR 0.013 0.001 TYR I 54 PHE 0.016 0.002 PHE I 104 TRP 0.006 0.001 TRP A 189 HIS 0.004 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00452 (19460) covalent geometry : angle 0.62455 (26369) hydrogen bonds : bond 0.04950 ( 1103) hydrogen bonds : angle 3.89552 ( 3399) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 760 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7680 (tpt-90) REVERT: A 97 GLN cc_start: 0.9037 (tp40) cc_final: 0.8768 (mm-40) REVERT: A 134 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7295 (pp20) REVERT: A 189 TRP cc_start: 0.8276 (m100) cc_final: 0.7968 (m100) REVERT: B 97 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.8477 (mp10) REVERT: C 97 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8634 (mp10) REVERT: D 179 GLN cc_start: 0.9045 (tp40) cc_final: 0.8783 (mm-40) REVERT: H 59 GLU cc_start: 0.8287 (mp0) cc_final: 0.8019 (mp0) REVERT: H 85 GLU cc_start: 0.7715 (tp30) cc_final: 0.7468 (tp30) REVERT: H 87 MET cc_start: 0.6754 (mpt) cc_final: 0.6382 (mpt) REVERT: H 146 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.6450 (mpt) REVERT: I 104 PHE cc_start: 0.4384 (OUTLIER) cc_final: 0.3746 (m-80) REVERT: J 61 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7968 (mtp-110) REVERT: J 104 PHE cc_start: 0.4520 (OUTLIER) cc_final: 0.3981 (m-80) REVERT: J 146 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.7183 (mpt) REVERT: J 200 ARG cc_start: 0.7893 (mtm180) cc_final: 0.7623 (mtm180) REVERT: K 104 PHE cc_start: 0.4524 (OUTLIER) cc_final: 0.3905 (m-80) REVERT: K 185 GLU cc_start: 0.7713 (tt0) cc_final: 0.7196 (tt0) REVERT: L 59 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8223 (mm-30) REVERT: L 60 GLU cc_start: 0.7961 (mp0) cc_final: 0.7349 (mp0) REVERT: L 135 VAL cc_start: 0.6846 (t) cc_final: 0.6530 (p) REVERT: M 60 GLU cc_start: 0.7998 (mp0) cc_final: 0.7701 (mp0) REVERT: N 59 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8049 (mp0) REVERT: N 75 ASN cc_start: 0.8624 (m-40) cc_final: 0.8387 (m110) REVERT: N 181 ARG cc_start: 0.8706 (tmm-80) cc_final: 0.8485 (ttt180) outliers start: 121 outliers final: 62 residues processed: 818 average time/residue: 0.6266 time to fit residues: 574.4258 Evaluate side-chains 817 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 743 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 61 ARG Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 58 PHE Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 126 MET Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 161 GLU Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 216 SER Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 208 ILE Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 44 optimal weight: 5.9990 chunk 232 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 224 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 223 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 201 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 166 optimal weight: 0.0060 overall best weight: 2.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 139 GLN A 171 GLN A 179 GLN B 58 ASN B 171 GLN B 179 GLN C 138 HIS C 179 GLN D 58 ASN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN E 132 ASN E 138 HIS F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 50 GLN G 58 ASN G 116 GLN H 98 ASN H 157 GLN I 75 ASN K 68 GLN K 75 ASN K 98 ASN L 75 ASN ** L 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 ASN N 115 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.110026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.100649 restraints weight = 27874.785| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.78 r_work: 0.3448 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 19460 Z= 0.207 Angle : 0.642 10.758 26369 Z= 0.330 Chirality : 0.044 0.168 3073 Planarity : 0.005 0.049 3451 Dihedral : 5.342 53.247 2724 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 5.63 % Allowed : 25.29 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.17), residues: 2478 helix: 2.04 (0.14), residues: 1365 sheet: 1.40 (0.33), residues: 217 loop : -0.60 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 188 TYR 0.013 0.002 TYR I 54 PHE 0.018 0.002 PHE N 104 TRP 0.004 0.001 TRP B 189 HIS 0.004 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00510 (19460) covalent geometry : angle 0.64231 (26369) hydrogen bonds : bond 0.05129 ( 1103) hydrogen bonds : angle 3.88547 ( 3399) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 765 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7742 (tpt-90) REVERT: A 97 GLN cc_start: 0.9089 (tp40) cc_final: 0.8823 (mm-40) REVERT: B 97 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.8489 (mp10) REVERT: C 97 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.8635 (mp10) REVERT: D 179 GLN cc_start: 0.9037 (tp40) cc_final: 0.8772 (mm-40) REVERT: H 59 GLU cc_start: 0.8296 (mp0) cc_final: 0.8030 (mp0) REVERT: H 87 MET cc_start: 0.6837 (mpt) cc_final: 0.6419 (mpt) REVERT: H 104 PHE cc_start: 0.4387 (OUTLIER) cc_final: 0.3241 (m-80) REVERT: H 146 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.6458 (mpt) REVERT: I 104 PHE cc_start: 0.4466 (OUTLIER) cc_final: 0.3502 (m-80) REVERT: J 61 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7955 (mtp-110) REVERT: J 104 PHE cc_start: 0.4572 (OUTLIER) cc_final: 0.3939 (m-80) REVERT: J 146 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.7352 (mpt) REVERT: J 200 ARG cc_start: 0.7892 (mtm180) cc_final: 0.7640 (mtm180) REVERT: K 104 PHE cc_start: 0.4530 (OUTLIER) cc_final: 0.3845 (m-80) REVERT: L 59 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8230 (mm-30) REVERT: L 60 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: L 135 VAL cc_start: 0.6892 (t) cc_final: 0.6562 (p) REVERT: L 181 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8503 (ttt90) REVERT: M 60 GLU cc_start: 0.8074 (mp0) cc_final: 0.7757 (mp0) REVERT: M 104 PHE cc_start: 0.4624 (OUTLIER) cc_final: 0.3266 (m-80) REVERT: M 146 MET cc_start: 0.8658 (mpt) cc_final: 0.8175 (mmt) REVERT: N 59 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8012 (mp0) REVERT: N 104 PHE cc_start: 0.4485 (OUTLIER) cc_final: 0.4160 (m-80) REVERT: N 164 ARG cc_start: 0.5603 (OUTLIER) cc_final: 0.5205 (ttm110) REVERT: N 181 ARG cc_start: 0.8652 (tmm-80) cc_final: 0.8429 (ttt180) outliers start: 115 outliers final: 60 residues processed: 820 average time/residue: 0.6431 time to fit residues: 589.7100 Evaluate side-chains 821 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 744 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 104 PHE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain J residue 61 ARG Chi-restraints excluded: chain J residue 83 CYS Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 225 SER Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 161 GLU Chi-restraints excluded: chain L residue 181 ARG Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 104 PHE Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 216 SER Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain M residue 227 ARG Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 104 PHE Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 160 SER Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 208 ILE Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 173 optimal weight: 7.9990 chunk 209 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 168 optimal weight: 0.7980 chunk 192 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 182 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 58 ASN A 171 GLN A 179 GLN B 38 ASN B 58 ASN B 179 GLN C 179 GLN D 58 ASN D 139 GLN E 58 ASN E 63 GLN E 132 ASN F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 58 ASN G 179 GLN H 157 GLN I 75 ASN K 75 ASN L 75 ASN L 115 GLN L 156 HIS M 75 ASN N 75 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.113045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.103646 restraints weight = 27863.919| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.80 r_work: 0.3479 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19460 Z= 0.126 Angle : 0.592 10.246 26369 Z= 0.300 Chirality : 0.042 0.151 3073 Planarity : 0.005 0.040 3451 Dihedral : 4.893 52.538 2720 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 5.19 % Allowed : 26.66 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.18), residues: 2478 helix: 2.31 (0.15), residues: 1358 sheet: 1.37 (0.34), residues: 217 loop : -0.59 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 182 TYR 0.011 0.001 TYR G 98 PHE 0.012 0.001 PHE H 104 TRP 0.010 0.001 TRP G 189 HIS 0.003 0.001 HIS L 156 Details of bonding type rmsd covalent geometry : bond 0.00298 (19460) covalent geometry : angle 0.59154 (26369) hydrogen bonds : bond 0.03915 ( 1103) hydrogen bonds : angle 3.65803 ( 3399) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 740 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7543 (tpt-90) REVERT: E 211 MET cc_start: 0.6935 (mtp) cc_final: 0.6662 (mtt) REVERT: G 134 GLU cc_start: 0.8533 (pt0) cc_final: 0.8091 (pt0) REVERT: G 189 TRP cc_start: 0.8386 (m100) cc_final: 0.7955 (m100) REVERT: H 59 GLU cc_start: 0.8185 (mp0) cc_final: 0.7933 (mp0) REVERT: H 87 MET cc_start: 0.6830 (mpt) cc_final: 0.6428 (mpt) REVERT: H 104 PHE cc_start: 0.4407 (OUTLIER) cc_final: 0.3349 (m-80) REVERT: H 179 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7935 (tmm-80) REVERT: H 227 ARG cc_start: 0.6130 (OUTLIER) cc_final: 0.5640 (tpt90) REVERT: I 104 PHE cc_start: 0.4504 (OUTLIER) cc_final: 0.3674 (m-80) REVERT: J 61 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7940 (mtp-110) REVERT: J 104 PHE cc_start: 0.4612 (OUTLIER) cc_final: 0.4172 (m-80) REVERT: J 200 ARG cc_start: 0.7893 (mtm180) cc_final: 0.7655 (mtm180) REVERT: K 104 PHE cc_start: 0.4458 (OUTLIER) cc_final: 0.3835 (m-80) REVERT: K 204 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8004 (tm-30) REVERT: L 59 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: L 60 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: L 128 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8121 (pt0) REVERT: L 135 VAL cc_start: 0.6798 (t) cc_final: 0.6522 (p) REVERT: L 161 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6879 (pm20) REVERT: M 60 GLU cc_start: 0.8045 (mp0) cc_final: 0.7751 (mp0) REVERT: M 146 MET cc_start: 0.8663 (mpt) cc_final: 0.8449 (mmt) REVERT: N 59 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7972 (mp0) REVERT: N 164 ARG cc_start: 0.5532 (OUTLIER) cc_final: 0.5157 (ttm110) REVERT: N 181 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8424 (ttt180) REVERT: N 185 GLU cc_start: 0.7566 (tt0) cc_final: 0.7359 (tt0) REVERT: N 200 ARG cc_start: 0.7728 (ttm110) cc_final: 0.7517 (mtm110) outliers start: 106 outliers final: 51 residues processed: 789 average time/residue: 0.6357 time to fit residues: 560.5414 Evaluate side-chains 801 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 735 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 104 PHE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain J residue 61 ARG Chi-restraints excluded: chain J residue 83 CYS Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 128 GLN Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 161 GLU Chi-restraints excluded: chain L residue 185 GLU Chi-restraints excluded: chain L residue 208 ILE Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain M residue 227 ARG Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 181 ARG Chi-restraints excluded: chain N residue 208 ILE Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 210 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 192 optimal weight: 10.0000 chunk 228 optimal weight: 0.3980 chunk 218 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 171 GLN A 179 GLN B 58 ASN B 171 GLN B 179 GLN C 50 GLN C 58 ASN C 179 GLN D 58 ASN D 179 GLN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN E 132 ASN F 35 GLN F 58 ASN F 171 GLN F 179 GLN G 179 GLN H 98 ASN H 157 GLN H 222 GLN I 75 ASN ** K 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 ASN L 75 ASN ** L 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 ASN N 75 ASN N 115 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.110779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.101447 restraints weight = 27696.683| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.79 r_work: 0.3445 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19460 Z= 0.179 Angle : 0.635 11.115 26369 Z= 0.324 Chirality : 0.044 0.162 3073 Planarity : 0.005 0.041 3451 Dihedral : 4.951 53.969 2719 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 5.19 % Allowed : 27.25 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.17), residues: 2478 helix: 2.19 (0.14), residues: 1365 sheet: 1.25 (0.33), residues: 217 loop : -0.56 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 182 TYR 0.011 0.001 TYR J 159 PHE 0.018 0.002 PHE N 104 TRP 0.009 0.001 TRP C 189 HIS 0.004 0.001 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00438 (19460) covalent geometry : angle 0.63459 (26369) hydrogen bonds : bond 0.04749 ( 1103) hydrogen bonds : angle 3.77024 ( 3399) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 744 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7228 (tpt-90) REVERT: A 74 ASP cc_start: 0.8337 (m-30) cc_final: 0.8004 (m-30) REVERT: B 97 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.8460 (mp10) REVERT: C 97 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8663 (mp10) REVERT: E 211 MET cc_start: 0.7008 (mtp) cc_final: 0.6712 (mtt) REVERT: G 134 GLU cc_start: 0.8553 (pt0) cc_final: 0.8116 (pt0) REVERT: G 189 TRP cc_start: 0.8407 (m100) cc_final: 0.7946 (m100) REVERT: H 59 GLU cc_start: 0.8251 (mp0) cc_final: 0.7980 (mp0) REVERT: H 87 MET cc_start: 0.7055 (mpt) cc_final: 0.6595 (mpt) REVERT: H 104 PHE cc_start: 0.4468 (OUTLIER) cc_final: 0.3731 (m-80) REVERT: H 176 GLU cc_start: 0.8383 (tp30) cc_final: 0.8111 (tp30) REVERT: H 179 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7901 (tmm-80) REVERT: I 104 PHE cc_start: 0.4607 (OUTLIER) cc_final: 0.3506 (m-80) REVERT: I 208 ILE cc_start: 0.7047 (OUTLIER) cc_final: 0.6730 (mt) REVERT: J 61 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7940 (mtp180) REVERT: J 104 PHE cc_start: 0.4555 (OUTLIER) cc_final: 0.3918 (m-80) REVERT: J 200 ARG cc_start: 0.7878 (mtm180) cc_final: 0.7646 (mtm180) REVERT: K 104 PHE cc_start: 0.4591 (OUTLIER) cc_final: 0.3781 (m-80) REVERT: K 204 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8056 (tm-30) REVERT: L 59 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: L 60 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: L 128 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8177 (pt0) REVERT: L 135 VAL cc_start: 0.6748 (t) cc_final: 0.6476 (p) REVERT: M 60 GLU cc_start: 0.8081 (mp0) cc_final: 0.7781 (mp0) REVERT: M 104 PHE cc_start: 0.4272 (OUTLIER) cc_final: 0.3087 (m-80) REVERT: N 59 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8031 (mp0) REVERT: N 104 PHE cc_start: 0.4480 (OUTLIER) cc_final: 0.4118 (m-80) REVERT: N 164 ARG cc_start: 0.5522 (OUTLIER) cc_final: 0.5145 (ttm110) REVERT: N 181 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8429 (ttt180) REVERT: N 185 GLU cc_start: 0.7644 (tt0) cc_final: 0.7231 (tt0) REVERT: N 200 ARG cc_start: 0.7849 (ttm110) cc_final: 0.7401 (mtm110) outliers start: 106 outliers final: 61 residues processed: 791 average time/residue: 0.6305 time to fit residues: 558.8380 Evaluate side-chains 809 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 730 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 104 PHE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain J residue 61 ARG Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 128 GLN Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 225 SER Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 104 PHE Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain M residue 227 ARG Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 104 PHE Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 181 ARG Chi-restraints excluded: chain N residue 208 ILE Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 181 optimal weight: 5.9990 chunk 201 optimal weight: 0.8980 chunk 147 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 230 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 chunk 28 optimal weight: 0.0970 chunk 67 optimal weight: 3.9990 chunk 217 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 63 GLN A 171 GLN A 179 GLN B 38 ASN B 58 ASN B 179 GLN C 58 ASN C 179 GLN D 58 ASN D 138 HIS D 179 GLN E 58 ASN E 132 ASN E 139 GLN F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 50 GLN G 58 ASN G 179 GLN H 75 ASN I 75 ASN K 75 ASN L 75 ASN L 156 HIS M 75 ASN M 166 GLN N 75 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.115212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.105833 restraints weight = 28071.134| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.83 r_work: 0.3514 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19460 Z= 0.112 Angle : 0.593 13.097 26369 Z= 0.297 Chirality : 0.042 0.152 3073 Planarity : 0.004 0.040 3451 Dihedral : 4.601 51.952 2716 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.21 % Allowed : 28.33 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.18), residues: 2478 helix: 2.41 (0.15), residues: 1358 sheet: 1.54 (0.34), residues: 210 loop : -0.43 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 91 TYR 0.011 0.001 TYR A 98 PHE 0.009 0.001 PHE N 104 TRP 0.009 0.001 TRP C 189 HIS 0.003 0.001 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00260 (19460) covalent geometry : angle 0.59255 (26369) hydrogen bonds : bond 0.03357 ( 1103) hydrogen bonds : angle 3.56902 ( 3399) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 745 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7424 (tpt-90) REVERT: B 50 GLN cc_start: 0.8705 (pm20) cc_final: 0.8496 (pm20) REVERT: C 39 ARG cc_start: 0.7939 (mtt180) cc_final: 0.7632 (mtt-85) REVERT: E 211 MET cc_start: 0.7004 (mtp) cc_final: 0.6754 (mtt) REVERT: G 134 GLU cc_start: 0.8587 (pt0) cc_final: 0.8128 (pt0) REVERT: G 189 TRP cc_start: 0.8410 (m100) cc_final: 0.7984 (m100) REVERT: H 59 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: H 87 MET cc_start: 0.6936 (mpt) cc_final: 0.6486 (mpt) REVERT: H 179 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7997 (tmm-80) REVERT: I 104 PHE cc_start: 0.4499 (OUTLIER) cc_final: 0.3671 (m-80) REVERT: J 104 PHE cc_start: 0.4622 (OUTLIER) cc_final: 0.4257 (m-80) REVERT: J 200 ARG cc_start: 0.7843 (mtm180) cc_final: 0.7614 (mtm180) REVERT: K 104 PHE cc_start: 0.4371 (OUTLIER) cc_final: 0.3818 (m-80) REVERT: K 204 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8032 (tm-30) REVERT: L 59 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: L 60 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: L 135 VAL cc_start: 0.6781 (t) cc_final: 0.6505 (p) REVERT: L 223 VAL cc_start: 0.8734 (t) cc_final: 0.8459 (p) REVERT: M 60 GLU cc_start: 0.7986 (mp0) cc_final: 0.7684 (mp0) REVERT: M 104 PHE cc_start: 0.4240 (OUTLIER) cc_final: 0.3723 (m-80) REVERT: M 181 ARG cc_start: 0.8703 (ttp80) cc_final: 0.8420 (ttt180) REVERT: M 204 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8111 (tm-30) REVERT: N 59 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: N 164 ARG cc_start: 0.5391 (OUTLIER) cc_final: 0.5007 (ttm110) REVERT: N 185 GLU cc_start: 0.7593 (tt0) cc_final: 0.7122 (tt0) REVERT: N 200 ARG cc_start: 0.7778 (ttm110) cc_final: 0.7388 (mtm110) outliers start: 86 outliers final: 47 residues processed: 783 average time/residue: 0.6458 time to fit residues: 566.3270 Evaluate side-chains 777 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 719 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain J residue 83 CYS Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 225 SER Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 200 ARG Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain M residue 104 PHE Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 181 ARG Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 229 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 0.0170 chunk 109 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 201 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 171 GLN A 179 GLN B 58 ASN B 171 GLN B 179 GLN C 58 ASN C 63 GLN C 138 HIS C 179 GLN D 58 ASN D 138 HIS D 179 GLN E 58 ASN E 139 GLN E 171 GLN F 58 ASN F 171 GLN F 179 GLN G 50 GLN G 171 GLN G 179 GLN H 75 ASN ** H 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 ASN K 75 ASN K 98 ASN L 75 ASN L 98 ASN L 156 HIS L 175 ASN M 75 ASN M 166 GLN N 75 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.111787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.102590 restraints weight = 28305.304| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.79 r_work: 0.3485 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19460 Z= 0.155 Angle : 0.655 12.767 26369 Z= 0.327 Chirality : 0.043 0.239 3073 Planarity : 0.005 0.039 3451 Dihedral : 4.698 53.670 2714 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.40 % Allowed : 29.35 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.18), residues: 2478 helix: 2.32 (0.15), residues: 1365 sheet: 1.53 (0.34), residues: 210 loop : -0.38 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 44 TYR 0.017 0.001 TYR E 98 PHE 0.017 0.002 PHE N 104 TRP 0.012 0.001 TRP C 189 HIS 0.010 0.001 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00380 (19460) covalent geometry : angle 0.65546 (26369) hydrogen bonds : bond 0.04249 ( 1103) hydrogen bonds : angle 3.67937 ( 3399) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 749 time to evaluate : 0.755 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: A 44 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7632 (tpt-90) REVERT: B 97 GLN cc_start: 0.9222 (OUTLIER) cc_final: 0.8460 (mp10) REVERT: C 39 ARG cc_start: 0.7951 (mtt180) cc_final: 0.7658 (mtt-85) REVERT: D 211 MET cc_start: 0.6953 (ttp) cc_final: 0.6375 (ttm) REVERT: E 211 MET cc_start: 0.7020 (mtp) cc_final: 0.6743 (mtt) REVERT: F 134 GLU cc_start: 0.8533 (tt0) cc_final: 0.7734 (pt0) REVERT: G 134 GLU cc_start: 0.8599 (pt0) cc_final: 0.7745 (pt0) REVERT: G 189 TRP cc_start: 0.8424 (m100) cc_final: 0.7676 (m100) REVERT: G 206 THR cc_start: 0.8052 (m) cc_final: 0.7823 (p) REVERT: H 59 GLU cc_start: 0.8186 (mp0) cc_final: 0.7925 (mp0) REVERT: H 87 MET cc_start: 0.7078 (mpt) cc_final: 0.6602 (mpt) REVERT: H 179 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7921 (tmm-80) REVERT: I 78 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7466 (ttm) REVERT: I 104 PHE cc_start: 0.4643 (OUTLIER) cc_final: 0.3663 (m-80) REVERT: I 146 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.6329 (mmt) REVERT: J 104 PHE cc_start: 0.4615 (OUTLIER) cc_final: 0.4042 (m-80) REVERT: J 200 ARG cc_start: 0.7810 (mtm180) cc_final: 0.7577 (mtm180) REVERT: K 104 PHE cc_start: 0.4625 (OUTLIER) cc_final: 0.3927 (m-80) REVERT: K 146 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.7868 (mpt) REVERT: K 204 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8027 (tm-30) REVERT: L 59 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8089 (mp0) REVERT: L 60 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7526 (mp0) REVERT: L 135 VAL cc_start: 0.6763 (t) cc_final: 0.6511 (p) REVERT: M 60 GLU cc_start: 0.8055 (mp0) cc_final: 0.7766 (mp0) REVERT: M 78 MET cc_start: 0.7476 (ptm) cc_final: 0.7258 (ptm) REVERT: M 104 PHE cc_start: 0.4287 (OUTLIER) cc_final: 0.3589 (m-80) REVERT: M 181 ARG cc_start: 0.8728 (ttp80) cc_final: 0.8434 (ttt180) REVERT: N 59 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: N 85 GLU cc_start: 0.6088 (mt-10) cc_final: 0.5829 (mt-10) REVERT: N 164 ARG cc_start: 0.5563 (OUTLIER) cc_final: 0.5185 (ttm110) REVERT: N 179 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8162 (tmm-80) REVERT: N 181 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8428 (ttt180) REVERT: N 185 GLU cc_start: 0.7683 (tt0) cc_final: 0.7272 (tt0) REVERT: N 200 ARG cc_start: 0.7828 (ttm110) cc_final: 0.7394 (mtm110) outliers start: 90 outliers final: 53 residues processed: 787 average time/residue: 0.6466 time to fit residues: 570.3029 Evaluate side-chains 824 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 755 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 185 GLU Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain I residue 78 MET Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 225 SER Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 146 MET Chi-restraints excluded: chain K residue 200 ARG Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain M residue 104 PHE Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 179 ARG Chi-restraints excluded: chain N residue 181 ARG Chi-restraints excluded: chain N residue 208 ILE Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 133 optimal weight: 0.1980 chunk 117 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 239 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 204 optimal weight: 0.9990 chunk 191 optimal weight: 6.9990 chunk 238 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 171 GLN A 179 GLN B 38 ASN B 58 ASN B 179 GLN C 58 ASN C 63 GLN C 179 GLN D 58 ASN D 138 HIS D 179 GLN E 58 ASN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 80 ASN G 171 GLN G 179 GLN H 75 ASN H 98 ASN I 75 ASN K 75 ASN K 115 GLN L 75 ASN L 98 ASN L 156 HIS M 75 ASN ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.114249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.105027 restraints weight = 28230.705| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.81 r_work: 0.3526 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 19460 Z= 0.123 Angle : 0.648 13.155 26369 Z= 0.320 Chirality : 0.042 0.156 3073 Planarity : 0.004 0.037 3451 Dihedral : 4.629 52.293 2714 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.01 % Allowed : 30.04 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.17), residues: 2478 helix: 2.39 (0.14), residues: 1358 sheet: 1.61 (0.34), residues: 210 loop : -0.36 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 182 TYR 0.012 0.001 TYR D 98 PHE 0.009 0.001 PHE H 104 TRP 0.016 0.001 TRP F 189 HIS 0.005 0.001 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00293 (19460) covalent geometry : angle 0.64834 (26369) hydrogen bonds : bond 0.03527 ( 1103) hydrogen bonds : angle 3.62084 ( 3399) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 751 time to evaluate : 0.791 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: A 44 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7451 (tpt-90) REVERT: C 39 ARG cc_start: 0.7914 (mtt180) cc_final: 0.7635 (mtt-85) REVERT: D 205 MET cc_start: 0.7914 (pmm) cc_final: 0.7672 (pmm) REVERT: D 211 MET cc_start: 0.6951 (ttp) cc_final: 0.6406 (ttm) REVERT: E 179 GLN cc_start: 0.8373 (tp40) cc_final: 0.8081 (tp-100) REVERT: E 211 MET cc_start: 0.7012 (mtp) cc_final: 0.6791 (mtt) REVERT: G 134 GLU cc_start: 0.8566 (pt0) cc_final: 0.7702 (pt0) REVERT: G 189 TRP cc_start: 0.8423 (m100) cc_final: 0.7697 (m100) REVERT: H 59 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: H 87 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6558 (mpt) REVERT: H 179 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7997 (tmm-80) REVERT: I 59 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: I 104 PHE cc_start: 0.4548 (OUTLIER) cc_final: 0.3765 (m-80) REVERT: I 135 VAL cc_start: 0.6515 (t) cc_final: 0.6193 (p) REVERT: I 146 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.6371 (mmt) REVERT: J 104 PHE cc_start: 0.4655 (OUTLIER) cc_final: 0.4249 (m-80) REVERT: J 181 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8209 (ttm-80) REVERT: K 104 PHE cc_start: 0.4452 (OUTLIER) cc_final: 0.3903 (m-80) REVERT: K 204 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7996 (tm-30) REVERT: L 59 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8089 (mp0) REVERT: L 60 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: L 135 VAL cc_start: 0.6810 (t) cc_final: 0.6505 (p) REVERT: M 60 GLU cc_start: 0.7996 (mp0) cc_final: 0.7694 (mp0) REVERT: M 104 PHE cc_start: 0.4280 (OUTLIER) cc_final: 0.3786 (m-80) REVERT: M 181 ARG cc_start: 0.8751 (ttp80) cc_final: 0.8456 (ttt180) REVERT: M 204 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8048 (tm-30) REVERT: N 59 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8039 (mp0) REVERT: N 164 ARG cc_start: 0.5512 (OUTLIER) cc_final: 0.5135 (ttm110) REVERT: N 181 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8459 (ttt180) REVERT: N 185 GLU cc_start: 0.7617 (tt0) cc_final: 0.7208 (tt0) REVERT: N 200 ARG cc_start: 0.7812 (ttm110) cc_final: 0.7399 (mtm110) outliers start: 82 outliers final: 51 residues processed: 783 average time/residue: 0.6265 time to fit residues: 549.6909 Evaluate side-chains 799 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 732 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 185 GLU Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 181 ARG Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 225 SER Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 200 ARG Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 104 PHE Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 181 ARG Chi-restraints excluded: chain N residue 208 ILE Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 59 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 229 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 144 optimal weight: 0.6980 chunk 104 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 171 GLN A 179 GLN B 38 ASN B 58 ASN B 171 GLN B 179 GLN C 58 ASN C 63 GLN C 179 GLN D 58 ASN D 138 HIS D 179 GLN E 58 ASN F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 50 GLN G 171 GLN G 179 GLN H 98 ASN ** H 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 ASN K 75 ASN K 98 ASN L 75 ASN L 98 ASN L 156 HIS L 175 ASN N 75 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.111968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.102686 restraints weight = 28135.111| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.79 r_work: 0.3493 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19460 Z= 0.153 Angle : 0.687 12.699 26369 Z= 0.341 Chirality : 0.044 0.163 3073 Planarity : 0.005 0.040 3451 Dihedral : 4.685 53.097 2711 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.82 % Allowed : 30.58 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.17), residues: 2478 helix: 2.27 (0.14), residues: 1365 sheet: 1.61 (0.34), residues: 210 loop : -0.32 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 44 TYR 0.019 0.001 TYR E 98 PHE 0.017 0.002 PHE N 104 TRP 0.030 0.002 TRP F 189 HIS 0.021 0.001 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00371 (19460) covalent geometry : angle 0.68706 (26369) hydrogen bonds : bond 0.04168 ( 1103) hydrogen bonds : angle 3.69643 ( 3399) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 754 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7581 (tpt-90) REVERT: C 39 ARG cc_start: 0.7944 (mtt180) cc_final: 0.7676 (mtt-85) REVERT: D 205 MET cc_start: 0.7978 (pmm) cc_final: 0.7759 (pmm) REVERT: D 211 MET cc_start: 0.7006 (ttp) cc_final: 0.6464 (ttm) REVERT: E 179 GLN cc_start: 0.8370 (tp40) cc_final: 0.8116 (tp-100) REVERT: E 211 MET cc_start: 0.7003 (mtp) cc_final: 0.6701 (mtt) REVERT: G 134 GLU cc_start: 0.8581 (pt0) cc_final: 0.7656 (pt0) REVERT: G 189 TRP cc_start: 0.8439 (m100) cc_final: 0.7656 (m100) REVERT: H 59 GLU cc_start: 0.8192 (mp0) cc_final: 0.7940 (mp0) REVERT: H 87 MET cc_start: 0.7025 (OUTLIER) cc_final: 0.6547 (mpt) REVERT: H 176 GLU cc_start: 0.8361 (tp30) cc_final: 0.8147 (tp30) REVERT: H 179 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7894 (tmm-80) REVERT: I 104 PHE cc_start: 0.4681 (OUTLIER) cc_final: 0.3762 (m-80) REVERT: I 146 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.6312 (mmt) REVERT: J 104 PHE cc_start: 0.4825 (OUTLIER) cc_final: 0.4243 (m-80) REVERT: J 181 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8190 (ttm-80) REVERT: K 104 PHE cc_start: 0.4431 (OUTLIER) cc_final: 0.3761 (m-80) REVERT: K 204 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7980 (tm-30) REVERT: L 59 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8110 (mp0) REVERT: L 60 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: L 135 VAL cc_start: 0.6772 (t) cc_final: 0.6512 (p) REVERT: M 60 GLU cc_start: 0.8022 (mp0) cc_final: 0.7725 (mp0) REVERT: M 104 PHE cc_start: 0.4347 (OUTLIER) cc_final: 0.3686 (m-80) REVERT: N 59 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: N 164 ARG cc_start: 0.5529 (OUTLIER) cc_final: 0.5154 (ttm110) REVERT: N 181 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8435 (ttt180) REVERT: N 185 GLU cc_start: 0.7640 (tt0) cc_final: 0.7242 (tt0) REVERT: N 200 ARG cc_start: 0.7796 (ttm110) cc_final: 0.7336 (mtm110) outliers start: 78 outliers final: 54 residues processed: 784 average time/residue: 0.6486 time to fit residues: 569.5957 Evaluate side-chains 818 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 750 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 185 GLU Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 181 ARG Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 225 SER Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 200 ARG Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 78 MET Chi-restraints excluded: chain M residue 104 PHE Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 181 ARG Chi-restraints excluded: chain N residue 208 ILE Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 36 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 185 optimal weight: 0.8980 chunk 183 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 chunk 240 optimal weight: 0.7980 chunk 188 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 125 optimal weight: 0.0770 chunk 81 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 63 GLN A 171 GLN A 179 GLN B 38 ASN B 179 GLN C 58 ASN C 63 GLN C 179 GLN D 58 ASN D 138 HIS D 179 GLN E 139 GLN F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 50 GLN G 132 ASN G 171 GLN G 179 GLN I 75 ASN K 75 ASN K 98 ASN L 75 ASN L 156 HIS M 75 ASN M 166 GLN N 75 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.114792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.105367 restraints weight = 28102.597| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.82 r_work: 0.3526 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19460 Z= 0.119 Angle : 0.666 13.012 26369 Z= 0.327 Chirality : 0.043 0.160 3073 Planarity : 0.004 0.038 3451 Dihedral : 4.573 53.702 2711 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.47 % Allowed : 30.97 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.18), residues: 2478 helix: 2.40 (0.14), residues: 1358 sheet: 1.51 (0.34), residues: 217 loop : -0.35 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 91 TYR 0.018 0.001 TYR H 159 PHE 0.010 0.001 PHE E 128 TRP 0.020 0.002 TRP F 189 HIS 0.004 0.001 HIS L 156 Details of bonding type rmsd covalent geometry : bond 0.00280 (19460) covalent geometry : angle 0.66610 (26369) hydrogen bonds : bond 0.03439 ( 1103) hydrogen bonds : angle 3.61558 ( 3399) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10304.18 seconds wall clock time: 175 minutes 28.54 seconds (10528.54 seconds total)